From 001fdad5683e5f0c5f38b2636c2c9458190a01cd Mon Sep 17 00:00:00 2001
From: gravesti <gravesti@users.noreply.github.com>
Date: Fri, 19 Jul 2024 07:27:08 +0000
Subject: [PATCH] deploy: 084a0cbc1c86c83e46fc5101b4ea796f26eb808a

---
 main/coverage-report/index.html | 18662 +++++++++++++++++-------------
 1 file changed, 10311 insertions(+), 8351 deletions(-)

diff --git a/main/coverage-report/index.html b/main/coverage-report/index.html
index 83d2d8be..d79ec520 100644
--- a/main/coverage-report/index.html
+++ b/main/coverage-report/index.html
@@ -95,7 +95,7 @@
   font-size: 11px;
 }</style>
   <div class="col-md-8 col-md-offset-2">
-    <h2>maicplus coverage - 54.75%</h2>
+    <h2>maicplus coverage - 58.55%</h2>
     <div class="tabbable">
       <ul class="nav nav-tabs" data-tabsetid="covr">
         <li class="active">
@@ -107,376 +107,376 @@ <h2>maicplus coverage - 54.75%</h2>
       </ul>
       <div class="tab-content" data-tabsetid="covr">
         <div class="tab-pane active" title="Files" data-value="Files" id="tab-covr-1">
-          <div class="datatables html-widget html-fill-item" id="htmlwidget-25c9cf39fbfd1b6d68ff" style="width:100%;height:500px;"></div>
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+          <div class="datatables html-widget html-fill-item" id="htmlwidget-98ffcf7d77d1295c404a" style="width:100%;height:500px;"></div>
+          <script type="application/json" data-for="htmlwidget-98ffcf7d77d1295c404a">{"x":{"filter":"none","vertical":false,"fillContainer":false,"data":[["<a href=\"#\">R/bootstrap.R<\/a>","<a href=\"#\">R/data_generation.R<\/a>","<a href=\"#\">R/zzz.R<\/a>","<a href=\"#\">R/utils.R<\/a>","<a href=\"#\">R/plot_km.R<\/a>","<a href=\"#\">R/matching.R<\/a>","<a href=\"#\">R/time-helper.R<\/a>","<a href=\"#\">R/process_data.R<\/a>","<a href=\"#\">R/plot_km2.R<\/a>","<a href=\"#\">R/binary-helper.R<\/a>","<a href=\"#\">R/maic_anchored.R<\/a>","<a href=\"#\">R/maic_unanchored.R<\/a>","<a href=\"#\">R/survival-helper.R<\/a>","<a href=\"#\">R/bucher.R<\/a>","<a href=\"#\">R/reporting.R<\/a>"],[89,74,3,21,749,532,55,281,210,86,554,432,83,191,112],[21,20,1,12,387,224,9,97,95,50,316,224,28,54,56],[0,0,0,2,67,91,5,55,76,43,273,195,25,49,56],[21,20,1,10,320,133,4,42,19,7,43,29,3,5,0],["0","0","0","2","0","34","11","5","1","2","7","20","10","32","12"],["0.00%","0.00%","0.00%","16.67%","17.31%","40.62%","55.56%","56.70%","80.00%","86.00%","86.39%","87.05%","89.29%","90.74%","100.00%"]],"container":"<table class=\"row-border\">\n  <thead>\n    <tr>\n      <th>File<\/th>\n      <th>Lines<\/th>\n      <th>Relevant<\/th>\n      <th>Covered<\/th>\n      <th>Missed<\/th>\n      <th>Hits / Line<\/th>\n      <th>Coverage<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"searching":false,"dom":"t","paging":false,"columnDefs":[{"targets":6,"createdCell":"function(td, cellData, rowData, row, col) {\n  var percent = cellData.replace(\"%\", \"\");\n  if (percent > 90) {\n    var grad = \"linear-gradient(90deg, #edfde7 \" + cellData + \", white \" + cellData + \")\";\n  } else if (percent > 75) {\n    var grad = \"linear-gradient(90deg, #f9ffe5 \" + cellData + \", white \" + cellData + \")\";\n  } else {\n    var grad = \"linear-gradient(90deg, #fcece9 \" + cellData + \", white \" + cellData + \")\";\n  }\n  $(td).css(\"background\", grad);\n}\n"},{"className":"dt-right","targets":[1,2,3,4]},{"name":"File","targets":0},{"name":"Lines","targets":1},{"name":"Relevant","targets":2},{"name":"Covered","targets":3},{"name":"Missed","targets":4},{"name":"Hits / Line","targets":5},{"name":"Coverage","targets":6}],"order":[],"autoWidth":false,"orderClasses":false},"callback":"function(table) {\ntable.on('click.dt', 'a', function() {\n  files = $('div#files div');\n  files.not('div.hidden').addClass('hidden');\n  id = $(this).text();\n  files.filter('div[id=\\'' + id + '\\']').removeClass('hidden');\n  $('ul.nav a[data-value=Source]').text(id).tab('show');\n});\n}"},"evals":["options.columnDefs.0.createdCell","callback"],"jsHooks":[]}</script>
         </div>
         <div class="tab-pane" title="Source" data-value="Source" id="tab-covr-2">
           <div id="files">
-            <div id="R/plot_km.R" class="hidden">
+            <div id="R/process_data.R" class="hidden">
               <table class="table-condensed">
                 <tbody>
                   <tr class="never">
                     <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Kaplan Meier (KM) plot function for anchored and unanchored cases</pre>
+                      <pre class="language-r"># Functions for pre-processing data before conduct MAIC</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' It is wrapper function of \code{basic_kmplot}. The argument setting is similar to \code{maic_anchored} and</pre>
+                      <pre class="language-r"># Functions to be exported ---------------------------------------</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' \code{maic_unanchored}, and it is used in those two functions.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' Pre-process aggregate data</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param weights_object an object returned by \code{estimate_weight}</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param tte_ipd a data frame of individual patient data (IPD) of internal trial, contain at least `"USUBJID"`,</pre>
+                      <pre class="language-r">#' This function checks the format of the aggregate data.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   `"EVENT"`, `"TIME"` columns and a column indicating treatment assignment</pre>
+                      <pre class="language-r">#' Data is required to have three columns: STUDY, ARM, and N.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param tte_pseudo_ipd a data frame of pseudo IPD by digitized KM curves of external trial (for time-to-event</pre>
+                      <pre class="language-r">#' Column names that do not have legal suffixes (MEAN, MEDIAN, SD, COUNT, or PROP) are dropped.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   endpoint), contain at least `"EVENT"`, `"TIME"`</pre>
+                      <pre class="language-r">#' If a variable is a count variable, it is converted to proportions by dividing the sample size (N).</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_ipd  a string, name of the interested investigation arm in internal trial \code{dat_igd} (real IPD)</pre>
+                      <pre class="language-r">#' Note, when the count is specified, proportion is always calculated based on the count, that is,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_agd a string, name of the interested investigation arm in external trial \code{dat_pseudo} (pseudo IPD)</pre>
+                      <pre class="language-r">#' specified proportion will be ignored if applicable.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_common a string, name of the common comparator in internal and external trial, by default is NULL,</pre>
+                      <pre class="language-r">#' If the aggregated data comes from multiple sources (i.e. different analysis population) and</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   indicating unanchored case</pre>
+                      <pre class="language-r">#' sample size differs for each variable, one option is to specify proportion directly instead of count by using suffix</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_var_ipd a string, column name in \code{tte_ipd} that contains the treatment assignment</pre>
+                      <pre class="language-r">#' _PROP.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_var_agd a string, column name in \code{tte_pseudo_ipd} that contains the treatment assignment</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param km_conf_type a string, pass to \code{conf.type} of \code{survfit}</pre>
+                      <pre class="language-r">#' @param raw_agd raw aggregate data should contain STUDY, ARM, and N. Variable names should be followed</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param km_layout a string, only applicable for unanchored case (\code{trt_common = NULL}), indicated the desired</pre>
+                      <pre class="language-r">#' by legal suffixes (i.e. MEAN, MEDIAN, SD, COUNT, or PROP).</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   layout of output KM curve.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ... other arguments in \code{basic_kmplot}</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' target_pop &lt;- read.csv(system.file("extdata", "aggregate_data_example_1.csv",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return In unanchored case, a KM plot with risk set table. In anchored case, depending on \code{km_layout},</pre>
+                      <pre class="language-r">#'   package = "maicplus", mustWork = TRUE</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' \itemize{</pre>
+                      <pre class="language-r">#' ))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item if "by_trial", 2 by 1 plot, first all KM curves (incl. weighted) in IPD trial, and then KM curves in AgD</pre>
+                      <pre class="language-r">#' target_pop2 &lt;- read.csv(system.file("extdata", "aggregate_data_example_2.csv",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   trial, with risk set table.</pre>
+                      <pre class="language-r">#'   package = "maicplus", mustWork = TRUE</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item if "by_arm", 2 by 1 plot, first KM curves of \code{trt_agd} and  \code{trt_ipd} (with and without weights),</pre>
+                      <pre class="language-r">#' ))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'    and then KM curves of \code{trt_common} in AgD trial and IPD trial (with and without weights). Risk set table is</pre>
+                      <pre class="language-r">#' target_pop3 &lt;- read.csv(system.file("extdata", "aggregate_data_example_3.csv",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     appended.</pre>
+                      <pre class="language-r">#'   package = "maicplus", mustWork = TRUE</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item if "all", 2 by 2 plot, all plots in "by_trial" and "by_arm" without risk set table appended.</pre>
+                      <pre class="language-r">#' ))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @example inst/examples/kmplot_anchored_ex.R</pre>
+                      <pre class="language-r">#' target_pop &lt;- process_agd(target_pop)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @example inst/examples/kmplot_unanchored_ex.R</pre>
+                      <pre class="language-r">#' target_pop2 &lt;- process_agd(target_pop2)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' target_pop3 &lt;- process_agd(target_pop3)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">kmplot &lt;- function(weights_object,</pre>
+                      <pre class="language-r">#' @return pre-processed aggregate level data</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                   tte_ipd,</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                   tte_pseudo_ipd,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                   trt_ipd,</pre>
+                      <pre class="language-r">process_agd &lt;- function(raw_agd) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">39</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                   trt_agd,</pre>
+                      <pre class="language-r">  raw_agd &lt;- as.data.frame(raw_agd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                   trt_common = NULL,</pre>
+                      <pre class="language-r">  # make all column names to be capital letters to avoid different style</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">41</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                   trt_var_ipd = "ARM",</pre>
+                      <pre class="language-r">  names(raw_agd) &lt;- toupper(names(raw_agd))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">42</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                   trt_var_agd = "ARM",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">43</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                   km_conf_type = "log-log",</pre>
+                      <pre class="language-r">  # define column name patterns[-]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">44</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                   km_layout = c("all", "by_trial", "by_arm"),</pre>
+                      <pre class="language-r">  must_exist &lt;- c("STUDY", "ARM", "N")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">45</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                   ...) {</pre>
+                      <pre class="language-r">  legal_suffix &lt;- c("MEAN", "MEDIAN", "SD", "COUNT", "PROP")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">46</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(tte_ipd) &lt;- toupper(names(tte_ipd))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">47</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(tte_pseudo_ipd) &lt;- toupper(names(tte_pseudo_ipd))</pre>
+                      <pre class="language-r">  # swap "TREATMENT" column to "ARM", if applicable</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">48</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  trt_var_ipd &lt;- toupper(trt_var_ipd)</pre>
+                      <pre class="language-r">  if ("TREATMENT" %in% names(raw_agd) &amp;&amp; (!"ARM" %in% names(raw_agd))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">49</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  trt_var_agd &lt;- toupper(trt_var_agd)</pre>
+                      <pre class="language-r">    raw_agd$ARM &lt;- raw_agd$TREATMENT</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">50</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    raw_agd &lt;- raw_agd[, names(raw_agd) != "TREATMENT"]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">51</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
+                      <pre class="language-r">    warning("'TREATMENT' column is renamed as 'ARM'")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">52</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  on.exit(par(original_par))</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -490,21 +490,21 @@ <h2>maicplus coverage - 54.75%</h2>
                     <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # pre check</pre>
+                      <pre class="language-r">  # check: must exist</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">55</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!"maicplus_estimate_weights" %in% class(weights_object)) {</pre>
+                      <pre class="language-r">  if (!all(must_exist %in% names(raw_agd))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">56</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("weights_object should be an object returned by estimate_weights")</pre>
+                      <pre class="language-r">    stop("At least 1 of the must-exists columns (STUDY, ARM, N) cannot be found in raw_agd!")</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -514,9356 +514,9183 @@ <h2>maicplus coverage - 54.75%</h2>
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">58</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!all(c("USUBJID", "TIME", "EVENT", trt_var_ipd) %in% names(tte_ipd))) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">59</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("tte_ipd needs to include at least USUBJID, TIME, EVENT, ", trt_var_ipd)</pre>
+                      <pre class="language-r">  # check: legal suffix</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">60</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  other_colnames &lt;- setdiff(names(raw_agd), must_exist)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">61</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!all(c("TIME", "EVENT", trt_var_agd) %in% names(tte_pseudo_ipd))) {</pre>
+                      <pre class="language-r">  ind1 &lt;- grepl("_", other_colnames, fixed = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">62</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("tte_pseudo_ipd needs to include at least TIME, EVENT, ", trt_var_agd)</pre>
+                      <pre class="language-r">  ind2 &lt;- sapply(other_colnames, function(xx) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">63</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">21<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    tmp &lt;- unlist(strsplit(xx, split = "_"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">64</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">21<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  km_layout &lt;- match.arg(km_layout, choices = c("all", "by_trial", "by_arm"), several.ok = FALSE)</pre>
+                      <pre class="language-r">    tmp[length(tmp)] # this deployment is robust to the cases that there are multiple _ in the column name</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">65</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">66</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # preparing data</pre>
+                      <pre class="language-r">  ind2 &lt;- (ind2 %in% legal_suffix)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">67</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  is_anchored &lt;- !is.null(trt_common)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">68</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_ipd &lt;- tte_ipd[tte_ipd[[trt_var_ipd]] %in% c(trt_ipd, trt_common), , drop = FALSE]</pre>
+                      <pre class="language-r">  use_cols &lt;- other_colnames[ind1 &amp; ind2]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">69</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_pseudo_ipd &lt;- tte_pseudo_ipd[tte_pseudo_ipd[[trt_var_agd]] %in% c(trt_agd, trt_common), , drop = FALSE]</pre>
+                      <pre class="language-r">  use_agd &lt;- raw_agd[, c(must_exist, use_cols), drop = FALSE]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">70</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_ipd$weights &lt;- weights_object$data$weights[match(weights_object$data$USUBJID, tte_ipd$USUBJID)]</pre>
+                      <pre class="language-r">  if (!all(other_colnames %in% use_cols)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">71</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_pseudo_ipd$weights &lt;- 1</pre>
+                      <pre class="language-r">    warning(paste0(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">72</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      "following columns are ignored since it does not follow the naming conventions:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">73</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # generate plot</pre>
+                      <pre class="language-r">      paste(setdiff(other_colnames, use_cols), collapse = ",")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">74</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!is_anchored) {</pre>
+                      <pre class="language-r">    ))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">75</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ## unanchored case</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">76</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmobj_B &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_agd)),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">77</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = tte_pseudo_ipd,</pre>
+                      <pre class="language-r">  # If the aggregate data is divided by different arms, calculate pooled arm statistics using</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">78</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conf.type = km_conf_type</pre>
+                      <pre class="language-r">  # complete_agd function; complete statistics is specified by ARM=="Total"</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">79</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  if (!"total" %in% tolower(use_agd$ARM)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">80</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmobj_A &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
+                      <pre class="language-r">    use_agd &lt;- complete_agd(use_agd)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">81</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = tte_ipd,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">82</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conf.type = km_conf_type</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">83</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  # calculate percentage columns</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">84</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmobj_A_adj &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
+                      <pre class="language-r">  ind &lt;- grepl("_COUNT$", names(use_agd))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">85</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = tte_ipd,</pre>
+                      <pre class="language-r">  if (any(ind)) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">86</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conf.type = km_conf_type,</pre>
+                      <pre class="language-r">    for (i in which(ind)) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">87</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      weights = weights</pre>
+                      <pre class="language-r">      tmp_prop &lt;- use_agd[[i]] / use_agd$N</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">88</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">      # in case some count are not specified, but proportion are specified, copy over those proportions</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">89</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      # this also means, in case count is specified, proportion is ignored even it is specified</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">90</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmdat &lt;- do.call(</pre>
+                      <pre class="language-r">      prop_name_i &lt;- gsub("_COUNT$", "_PROP", names(use_agd)[i])</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">91</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      rbind,</pre>
+                      <pre class="language-r">      if (prop_name_i %in% names(use_agd)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">92</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      c(</pre>
+                      <pre class="language-r">        tmp_prop[is.na(tmp_prop)] &lt;- use_agd[is.na(tmp_prop), prop_name_i]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">93</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_B, trt_agd),</pre>
+                      <pre class="language-r">        names(use_agd)[names(use_agd) == prop_name_i] &lt;- paste0(prop_name_i, "_redundant")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">94</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_A, trt_ipd),</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">95</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_A_adj, paste(trt_ipd, "(weighted)"))</pre>
+                      <pre class="language-r">      use_agd[[i]] &lt;- tmp_prop</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">96</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">97</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    names(use_agd) &lt;- gsub("_COUNT$", "_PROP", names(use_agd))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">98</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmdat$treatment &lt;- factor(kmdat$treatment, levels = unique(kmdat$treatment))</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">99</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  use_agd &lt;- use_agd[, !grepl("_redundant$", names(use_agd))]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">100</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    basic_kmplot(kmdat,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">101</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      show_risk_set = TRUE,</pre>
+                      <pre class="language-r">  # output</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">102</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      main_title = "Kaplan-Meier Curves",</pre>
+                      <pre class="language-r">  with(use_agd, use_agd[tolower(ARM) == "total", , drop = FALSE])</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">103</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subplot_heights = NULL,</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">104</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      suppress_plot_layout = FALSE,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">105</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ...</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">106</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' Create dummy variables from categorical variables in an individual patient data (ipd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">107</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">108</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # anchored case</pre>
+                      <pre class="language-r">#' This is a convenient function to convert categorical variables into dummy binary variables.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # - agd trial km data</pre>
+                      <pre class="language-r">#' This would be especially useful if the variable has more than two factors.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">110</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmobj_C_S1 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_agd)),</pre>
+                      <pre class="language-r">#' Note that the original variable is kept after a variable is dummized.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">111</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = tte_pseudo_ipd,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">112</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conf.type = km_conf_type,</pre>
+                      <pre class="language-r">#' @param raw_ipd ipd data that contains variable to dummize</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">113</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_pseudo_ipd$", trt_var_agd, " == '", trt_common, "')")))</pre>
+                      <pre class="language-r">#' @param dummize_cols vector of column names to binarize</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">114</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' @param dummize_ref_level vector of reference level of the variables to binarize</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">115</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmobj_B_S1 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_agd)),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">116</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = tte_pseudo_ipd,</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">117</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conf.type = km_conf_type,</pre>
+                      <pre class="language-r">#' data(adsl_twt)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">118</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_pseudo_ipd$", trt_var_agd, " == '", trt_agd, "')")))</pre>
+                      <pre class="language-r">#' dummize_ipd(adsl_twt, dummize_cols = c("SEX"), dummize_ref_level = c("Male"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">119</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">120</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # - ipd trial km data</pre>
+                      <pre class="language-r">#' @return ipd with dummized columns</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">121</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmobj_C_S2 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">122</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = tte_ipd,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">123</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conf.type = km_conf_type,</pre>
+                      <pre class="language-r">dummize_ipd &lt;- function(raw_ipd, dummize_cols, dummize_ref_level) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">124</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_ipd$", trt_var_ipd, " == '", trt_common, "')")))</pre>
+                      <pre class="language-r">  for (i in seq_along(dummize_cols)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">125</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    yy &lt;- raw_ipd[[dummize_cols[i]]]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">126</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmobj_A_S2 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
+                      <pre class="language-r">    yy_levels &lt;- na.omit(unique(yy))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">127</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = tte_ipd,</pre>
+                      <pre class="language-r">    yy &lt;- factor(as.character(yy), levels = c(dummize_ref_level[i], setdiff(yy_levels, dummize_ref_level[i])))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">128</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conf.type = km_conf_type,</pre>
+                      <pre class="language-r">    new_yy &lt;- sapply(levels(yy)[-1], function(j) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">129</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_ipd$", trt_var_ipd, " == '", trt_ipd, "')")))</pre>
+                      <pre class="language-r">      as.numeric(yy == j)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">130</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">131</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # - ipd trial km data with weights</pre>
+                      <pre class="language-r">    new_yy &lt;- as.data.frame(new_yy)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">132</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmobj_Cadj_S2 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
+                      <pre class="language-r">    names(new_yy) &lt;- toupper(paste(dummize_cols[i], levels(yy)[-1], sep = "_"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">133</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = tte_ipd,</pre>
+                      <pre class="language-r">    raw_ipd &lt;- cbind(raw_ipd, new_yy)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">134</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conf.type = km_conf_type,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">135</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      weights = weights,</pre>
+                      <pre class="language-r">  raw_ipd</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">136</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_ipd$", trt_var_ipd, " == '", trt_common, "')")))</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">137</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">138</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmobj_Aadj_S2 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">139</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = tte_ipd,</pre>
+                      <pre class="language-r">#' Center individual patient data (IPD) variables using aggregate data averages</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">140</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conf.type = km_conf_type,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">141</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      weights = weights,</pre>
+                      <pre class="language-r">#' This function subtracts IPD variables (prognostic variables and/or effect modifiers)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">142</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_ipd$", trt_var_ipd, " == '", trt_ipd, "')")))</pre>
+                      <pre class="language-r">#' by the aggregate data averages. This centering is needed in order to calculate weights.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">143</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' IPD and aggregate data variable names should match.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # - plotdat for layout by trial</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">145</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmdat_s2 &lt;- do.call(</pre>
+                      <pre class="language-r">#' @param ipd IPD variable names should match the aggregate data names without the suffix.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">146</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      rbind,</pre>
+                      <pre class="language-r">#' This would involve either changing the aggregate data name or the ipd name.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">147</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      c(</pre>
+                      <pre class="language-r">#' For instance, if we binarize SEX variable with MALE as a reference using [dummize_ipd],</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">148</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_C_S2, trt_common),</pre>
+                      <pre class="language-r">#' function names the new variable as SEX_MALE.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">149</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_A_S2, trt_ipd),</pre>
+                      <pre class="language-r">#' In this case, SEX_MALE should also be available in the aggregate data.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">150</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_Aadj_S2, paste(trt_ipd, "(weighted)")),</pre>
+                      <pre class="language-r">#' @param agd pre-processed aggregate data which contain STUDY, ARM, and N. Variable names</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">151</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_Cadj_S2, paste(trt_common, "(weighted)"))</pre>
+                      <pre class="language-r">#' should be followed by legal suffixes (i.e. MEAN, MEDIAN, SD, or PROP). Note that COUNT</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">152</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' suffix is no longer accepted.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">153</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">154</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmdat_s2$treatment &lt;- factor(kmdat_s2$treatment, levels = unique(kmdat_s2$treatment))</pre>
+                      <pre class="language-r">#' # load in IPD</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">155</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmdat_s1 &lt;- do.call(</pre>
+                      <pre class="language-r">#' data(adsl_sat)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">156</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      rbind,</pre>
+                      <pre class="language-r">#' adsl &lt;- dummize_ipd(adsl_sat, dummize_cols = c("SEX"), dummize_ref_level = c("Female"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">157</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      c(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">158</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_C_S1, trt_common),</pre>
+                      <pre class="language-r">#' # Reading aggregate data by Excel</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">159</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_B_S1, trt_agd)</pre>
+                      <pre class="language-r">#' target_pop &lt;- read.csv(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">160</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#'   system.file("extdata", "aggregate_data_example_1.csv", package = "maicplus", mustWork = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">161</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">162</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmdat_s1$treatment &lt;- factor(kmdat_s1$treatment, levels = unique(kmdat_s1$treatment))</pre>
+                      <pre class="language-r">#' agd &lt;- process_agd(target_pop)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">163</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # - plotdat for layout by arm</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">164</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmdat_a2 &lt;- do.call(</pre>
+                      <pre class="language-r">#' # Alternatively, you can specify aggregate data manually in data frame</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">165</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      rbind,</pre>
+                      <pre class="language-r">#' data(agd)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">166</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      c(</pre>
+                      <pre class="language-r">#' ipd_centered &lt;- center_ipd(ipd = adsl, agd = agd)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">167</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_B_S1, trt_agd),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">168</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_A_S2, trt_ipd),</pre>
+                      <pre class="language-r">#' @return centered ipd using aggregate level data averages</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">169</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_Aadj_S2, paste(trt_ipd, "(weighted)"))</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">170</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">171</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">center_ipd &lt;- function(ipd, agd) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">172</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmdat_a2$treatment &lt;- factor(kmdat_a2$treatment, levels = unique(kmdat_a2$treatment))</pre>
+                      <pre class="language-r">  # regularized column name patterns</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">173</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmdat_a1 &lt;- do.call(</pre>
+                      <pre class="language-r">  must_exist &lt;- c("STUDY", "ARM", "N")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">174</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      rbind,</pre>
+                      <pre class="language-r">  legal_suffix &lt;- c("MEAN", "MEDIAN", "SD", "PROP")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">175</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      c(</pre>
+                      <pre class="language-r">  suffix_pat &lt;- paste(paste0("_", legal_suffix, "$"), collapse = "|")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">176</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_C_S1, paste(trt_common, "(AgD)")),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">177</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_C_S2, paste(trt_common, "(IPD)")),</pre>
+                      <pre class="language-r">  for (i in seq_len(nrow(agd))) { # study i</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">178</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        survfit_makeup(kmobj_Cadj_S2, paste(trt_common, "(IPD,weighted)"))</pre>
+                      <pre class="language-r">    study_id &lt;- agd$STUDY[i]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">179</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">    use_agd &lt;- agd[i, !names(agd) %in% must_exist, drop = FALSE]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">180</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    param_id &lt;- gsub(suffix_pat, "", names(use_agd))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">181</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmdat_a1$treatment &lt;- factor(kmdat_a1$treatment, levels = unique(kmdat_a1$treatment))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">182</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    for (j in seq_len(ncol(use_agd))) { # effect modifier j</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">183</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      if (is.na(use_agd[[j]])) next</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # make plot depending on the layout</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">185</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">56<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (km_layout == "by_trial") {</pre>
+                      <pre class="language-r">      ipd_param &lt;- param_id[j]</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">186</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # 1 by 2 plot, each plot is per trial</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">187</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">56<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subplot_heights &lt;- c(7, 0.7 + 2 * 0.7, 0.8)</pre>
+                      <pre class="language-r">      if (grepl("_MEAN$|_PROP$", names(use_agd)[j])) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">188</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">32<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      layout_mat &lt;- matrix(1:4, ncol = 2)</pre>
+                      <pre class="language-r">        ipd[[paste0(ipd_param, "_", "CENTERED")]] &lt;- ipd[[ipd_param]] - use_agd[[j]]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">189</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">24<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      layout(layout_mat, heights = subplot_heights)</pre>
+                      <pre class="language-r">      } else if (grepl("_MEDIAN$", names(use_agd)[j])) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">190</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">16<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        ipd[[paste0(ipd_param, "_MEDIAN_", "CENTERED")]] &lt;- ipd[[ipd_param]] &gt; use_agd[[j]]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">191</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">16<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      basic_kmplot(kmdat_s2,</pre>
+                      <pre class="language-r">        ipd[[paste0(ipd_param, "_MEDIAN_", "CENTERED")]] &lt;- ipd[[paste0(ipd_param, "_MEDIAN_", "CENTERED")]] - 0.5</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">192</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_common, ") in the IPD trial"),</pre>
+                      <pre class="language-r">      } else if (grepl("_SD$", names(use_agd)[j])) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">193</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
+                      <pre class="language-r">        ipd[[paste0(ipd_param, "_SQUARED_", "CENTERED")]] &lt;- ipd[[ipd_param]]^2</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">194</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">        tmp_aim &lt;- use_agd[[j]]^2 + (use_agd[[paste0(ipd_param, "_MEAN")]]^2)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">195</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        ipd[[paste0(ipd_param, "_SQUARED_", "CENTERED")]] &lt;- ipd[[paste0(ipd_param, "_SQUARED_", "CENTERED")]] - tmp_aim</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">196</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      basic_kmplot(kmdat_s1,</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">197</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_agd, " vs ", trt_common, ") in the AgD trial"),</pre>
+                      <pre class="language-r">    } # end of j</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">198</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
+                      <pre class="language-r">  } # end of i</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">199</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">200</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    } else if (km_layout == "by_arm") {</pre>
+                      <pre class="language-r">  # output</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">201</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # 1 by 2 plot, by 1 is for investigational arm, the other is for common comparator</pre>
+                      <pre class="language-r">  ipd</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">202</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subplot_heights &lt;- c(7, 0.7 + 2 * 0.7, 0.8)</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">203</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      layout_mat &lt;- matrix(1:4, ncol = 2)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">204</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      layout(layout_mat, heights = subplot_heights)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">205</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' Calculate pooled arm statistics in Aggregated Data (AgD) based on arm-specific statistics</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">206</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      basic_kmplot(kmdat_a2,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">207</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_agd, ")"),</pre>
+                      <pre class="language-r">#' This is a convenient function to pool arm statistics. This function is called</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">208</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
+                      <pre class="language-r">#' within process_agd and when the ARM is not equal to "Total". Note pooled</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">209</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' median can't be calculated and it is only an approximation.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">210</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">211</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      basic_kmplot(kmdat_a1,</pre>
+                      <pre class="language-r">#' @param use_agd aggregated data that is processed within process_agd</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">212</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves of Common Comparator \n", trt_common, "(IPD vs AgD Trial)"),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">213</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
+                      <pre class="language-r">#' @return Complete N, count, mean, sd, and median for the pooled arm</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">214</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">215</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    } else {</pre>
+                      <pre class="language-r">complete_agd &lt;- function(use_agd) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">216</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # 2 by 2 plot, combine by trial and by arm</pre>
+                      <pre class="language-r">  use_agd &lt;- as.data.frame(use_agd)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">217</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      layout_mat &lt;- matrix(1:4, ncol = 2, byrow = TRUE)</pre>
+                      <pre class="language-r">  use_agd &lt;- with(use_agd, {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">218</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      layout(layout_mat)</pre>
+                      <pre class="language-r">    use_agd[tolower(ARM) != "total", , drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">219</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">220</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      basic_kmplot(kmdat_s2,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">221</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_common, ") in the IPD trial"),</pre>
+                      <pre class="language-r">  if (nrow(use_agd) &lt; 2) stop("error in call complete_agd: need to have at least 2 rows that ARM!='total' ")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">222</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        show_risk_set = FALSE,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">223</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
+                      <pre class="language-r">  rowId &lt;- nrow(use_agd) + 1</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">224</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">  use_agd[rowId, ] &lt;- NA</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">225</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  use_agd$STUDY[rowId] &lt;- use_agd$STUDY[1]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">226</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      basic_kmplot(kmdat_s1,</pre>
+                      <pre class="language-r">  use_agd$ARM[rowId] &lt;- "total"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">227</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_agd, " vs ", trt_common, ") in the AgD trial"),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">228</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        show_risk_set = FALSE,</pre>
+                      <pre class="language-r">  # complete N and count</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">229</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
+                      <pre class="language-r">  NN &lt;- use_agd[["N"]][rowId] &lt;- sum(use_agd[["N"]], na.rm = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">230</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">  nn &lt;- use_agd[["N"]][-rowId]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">231</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  for (i in grep("_COUNT$", names(use_agd), value = TRUE)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">232</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      basic_kmplot(kmdat_a2,</pre>
+                      <pre class="language-r">    use_agd[[i]][rowId] &lt;- sum(use_agd[[i]][-rowId], na.rm = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">233</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_agd, ")"),</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">234</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        show_risk_set = FALSE,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">235</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
+                      <pre class="language-r">  # complete MEAN</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">236</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">  for (i in grep("_MEAN$", names(use_agd), value = TRUE)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">237</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    use_agd[[i]][rowId] &lt;- sum(use_agd[[i]][-rowId] * nn) / NN</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">238</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      basic_kmplot(kmdat_a1,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">239</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves of Common Comparator \n", trt_common, "(IPD vs AgD Trial)"),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">240</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        show_risk_set = FALSE,</pre>
+                      <pre class="language-r">  # complete SD</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">241</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
+                      <pre class="language-r">  for (i in grep("_SD$", names(use_agd), value = TRUE)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">242</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">    use_agd[[i]][rowId] &lt;- sqrt(sum(use_agd[[i]][-rowId]^2 * (nn - 1)) / (NN - 1))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">243</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">244</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">245</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  # complete MEDIAN, approximately!!</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">246</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  for (i in grep("_MEDIAN$", names(use_agd), value = TRUE)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">247</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    use_agd[[i]][rowId] &lt;- mean(use_agd[[i]][-rowId])</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">248</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Basic Kaplan Meier (KM) plot function</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">249</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">250</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This function can generate a basic KM plot with or without risk set table appended at the bottom. In a single plot,</pre>
+                      <pre class="language-r">  # output</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">251</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' it can include up to 4 KM curves. This depends on number of levels in 'treatment' column in the input data.frame</pre>
+                      <pre class="language-r">  use_agd</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">252</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' \code{kmdat}</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">253</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">254</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param kmdat a `data.frame`, must consist `treatment`, `time` (unit in days), `n.risk`, `censor`, `surv`, similar to</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">255</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   an output from \code{maicplus:::survfit_makeup}</pre>
+                      <pre class="language-r">#' helper function: transform TTE ADaM data to suitable input for survival R package</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">256</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param endpoint_name a string, name of time to event endpoint, to be show in the last line of title</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">257</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param time_scale a string, time unit of median survival time, taking a value of 'years', 'months', 'weeks' or 'days'</pre>
+                      <pre class="language-r">#' @param dd data frame, ADTTE read via `haven::read_sas`</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">258</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param time_grid a numeric vector in the unit of \code{time_scale}, risk set table and x axis of the km plot will be</pre>
+                      <pre class="language-r">#' @param time_scale a character string, 'years', 'months', 'weeks' or 'days', time unit of median survival time</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">259</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   defined based on this time grid</pre>
+                      <pre class="language-r">#' @param trt values to include in treatment column</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">260</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param show_risk_set logical, show risk set table or not, TRUE by default</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">261</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param main_title a string, main title of the KM plot</pre>
+                      <pre class="language-r">#' @return a data frame that can be used as input to `survival::Surv`</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">262</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param subplot_heights a numeric vector, heights argument to \code{graphic::layout()},NULL by default which means</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">263</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   user will use the default setting</pre>
+                      <pre class="language-r">ext_tte_transfer &lt;- function(dd, time_scale = "months", trt = NULL) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">264</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param suppress_plot_layout logical, suppress the layout setting in this function so that user can specify layout</pre>
+                      <pre class="language-r">  time_scale &lt;- match.arg(time_scale, choices = c("years", "months", "weeks", "days"))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">265</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   outside of the function, FALSE by default</pre>
+                      <pre class="language-r">  time_units &lt;- get_time_conversion(time_scale)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">266</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param use_colors a character vector of length up to 4, colors to the KM curves, it will be passed to `col` of</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">267</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \code{lines()}</pre>
+                      <pre class="language-r">  if ("CENSOR" %in% names(dd)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">268</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param use_line_types a numeric vector of length up to 4, line type to the KM curves, it will be passed to `lty` of</pre>
+                      <pre class="language-r">    dd &lt;- dd[!is.na(dd$CENSOR), ]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">269</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \code{lines()}</pre>
+                      <pre class="language-r">    dd$status &lt;- as.numeric(dd$CENSOR == 0)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">270</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param use_pch_cex a scalar between 0 and 1, point size to indicate censored individuals on the KM curves, it will be</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">271</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   passed to `cex` of \code{points()}</pre>
+                      <pre class="language-r">  if ("EVENT" %in% names(dd)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">272</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param use_pch_alpha a scalar between 0 and 255, degree of color transparency of points to indicate censored</pre>
+                      <pre class="language-r">    dd$status &lt;- as.numeric(as.character(dd$EVENT))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">273</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   individuals on the KM curves, it will be passed to `cex` of \code{points()}</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">274</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  if ("TIME" %in% names(dd)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">275</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @example inst/examples/basic_kmplot_ex.R</pre>
+                      <pre class="language-r">    dd$AVAL &lt;- as.numeric(as.character(dd$TIME))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">276</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">277</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a KM plot with or without risk set table appended at the bottom, with up to 4 KM curves</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">278</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">  dd$time &lt;- dd$AVAL * time_units</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">279</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  if (!is.null(trt)) dd$treatment &lt;- trt</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">280</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">basic_kmplot &lt;- function(kmdat,</pre>
+                      <pre class="language-r">  as.data.frame(dd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">281</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         endpoint_name = "Time to Event Endpoint",</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/maic_anchored.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
                   <tr class="never">
-                    <td class="num">282</td>
+                    <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         time_scale,</pre>
+                      <pre class="language-r">#' Anchored MAIC for binary and time-to-event endpoint</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">283</td>
+                    <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         time_grid,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">284</td>
+                    <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         show_risk_set = TRUE,</pre>
+                      <pre class="language-r">#' This is a wrapper function to provide adjusted effect estimates and relevant statistics in anchored case (i.e. there</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">285</td>
+                    <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         main_title = "Kaplan-Meier Curves",</pre>
+                      <pre class="language-r">#' is a common comparator arm in the internal and external trial).</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">286</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         subplot_heights = NULL,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">287</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         suppress_plot_layout = FALSE,</pre>
+                      <pre class="language-r">#' @param weights_object an object returned by \code{estimate_weight}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">288</td>
+                    <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         use_colors = NULL,</pre>
+                      <pre class="language-r">#' @param ipd a data frame that meet format requirements in 'Details', individual patient data (IPD) of internal trial</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">289</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         use_line_types = NULL,</pre>
+                      <pre class="language-r">#' @param pseudo_ipd a data frame, pseudo IPD from digitized KM curve of external trial (for time-to-event endpoint) or</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">290</td>
+                    <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         use_pch_cex = 0.65,</pre>
+                      <pre class="language-r">#'   from contingency table (for binary endpoint)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">291</td>
+                    <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         use_pch_alpha = 100) {</pre>
+                      <pre class="language-r">#' @param trt_ipd  a string, name of the interested investigation arm in internal trial \code{ipd} (internal IPD)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">292</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">11</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
+                      <pre class="language-r">#' @param trt_agd a string, name of the interested investigation arm in external trial \code{pseudo_ipd} (pseudo IPD)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">293</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">12</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  on.exit(par(original_par))</pre>
+                      <pre class="language-r">#' @param trt_common a string, name of the common comparator in internal and external trial</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">294</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param trt_var_ipd a string, column name in \code{ipd} that contains the treatment assignment</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">295</td>
+                    <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # precheck</pre>
+                      <pre class="language-r">#' @param trt_var_agd a string, column name in \code{ipd} that contains the treatment assignment</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">296</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">15</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!length(subplot_heights) %in% c(0, (1 + show_risk_set))) {</pre>
+                      <pre class="language-r">#' @param endpoint_type a string, one out of the following "binary", "tte" (time to event)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">297</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">16</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("length of subplot_heights should be ", (1 + show_risk_set))</pre>
+                      <pre class="language-r">#' @param endpoint_name a string, name of time to event endpoint, to be show in the last line of title</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">298</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' @param time_scale a string, time unit of median survival time, taking a value of 'years', 'months', 'weeks' or</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">299</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">18</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!is.factor(kmdat$treatment)) {</pre>
+                      <pre class="language-r">#'   'days'. NOTE: it is assumed that values in TIME column of \code{ipd} and \code{pseudo_ipd} is in the unit of days</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">300</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">19</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("kmdat$treatment needs to be a factor, its levels will be used in legend and title, first level is comparator")</pre>
+                      <pre class="language-r">#' @param km_conf_type a string, pass to \code{conf.type} of \code{survfit}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">301</td>
+                    <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' @param eff_measure a string, "RD" (risk difference), "OR" (odds ratio), "RR" (relative risk) for a binary endpoint;</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">302</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">21</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (nlevels(kmdat$treatment) &gt; 4) stop("kmdat$treatment cannot have more than 4 levels")</pre>
+                      <pre class="language-r">#'   "HR" for a time-to-event endpoint. By default is \code{NULL}, "OR" is used for binary case, otherwise "HR" is used.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">303</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">22</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(time_grid) &amp;&amp; show_risk_set) stop("please provide a numeric vector as time_grid to show risk set table")</pre>
+                      <pre class="language-r">#' @param boot_ci_type a string, one of `c("norm","basic", "stud", "perc", "bca")` to select the type of bootstrap</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">304</td>
+                    <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   confidence interval. See [boot::boot.ci] for more details.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">305</td>
+                    <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # set up x axis (time)</pre>
+                      <pre class="language-r">#' @param binary_robust_cov_type a string to pass to argument `type` of [sandwich::vcovHC], see possible options in the</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">306</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">25</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(time_grid)) {</pre>
+                      <pre class="language-r">#'   documentation of that function. Default is `"HC3"`</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">307</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">26</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    max_t &lt;- max(kmdat$time)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">308</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">27</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    t_range &lt;- c(0, get_time_as(max_t, time_scale) * 1.07)</pre>
+                      <pre class="language-r">#' @details It is required that input \code{ipd} and \code{pseudo_ipd} to have the following</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">309</td>
+                    <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">#'   columns. This function is not sensitive to upper or lower case of letters in column names.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">310</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">29</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    t_range &lt;- c(0, max(time_grid))</pre>
+                      <pre class="language-r">#' \itemize{</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">311</td>
+                    <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#'   \item USUBJID - character, unique subject ID</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">312</td>
+                    <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   \item ARM - character or factor, treatment indicator, column name does not have to be 'ARM'. User specify in</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">313</td>
+                    <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # plat layout in par</pre>
+                      <pre class="language-r">#'    \code{trt_var_ipd} and \code{trt_var_agd}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">314</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">33</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!suppress_plot_layout) {</pre>
+                      <pre class="language-r">#'  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">315</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">34</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    nr_subplot &lt;- (1 + show_risk_set)</pre>
+                      <pre class="language-r">#'  For time-to-event analysis, the follow columns are required:</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">316</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">35</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (is.null(subplot_heights)) subplot_heights &lt;- c(7, 0.7 + nlevels(kmdat$treatment) * 0.7, 0.8)</pre>
+                      <pre class="language-r">#'  \itemize{</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">317</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">36</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    layout_mat &lt;- matrix(1:nr_subplot, ncol = 1)</pre>
+                      <pre class="language-r">#'   \item EVENT - numeric, `1` for censored/death, `0` otherwise</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">318</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">37</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    layout(layout_mat, heights = subplot_heights)</pre>
+                      <pre class="language-r">#'   \item TIME - numeric column, observation time of the \code{EVENT}; unit in days</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">319</td>
+                    <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">320</td>
+                    <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' For binary outcomes:</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">321</td>
+                    <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # plot cosmetic setup</pre>
+                      <pre class="language-r">#' \itemize{</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">322</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">41</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(use_line_types)) {</pre>
+                      <pre class="language-r">#'   \item RESPONSE - numeric, `1` for event occurred, `0` otherwise</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">323</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">42</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_lty &lt;- c(1, 1, 2, 2)</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">324</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">43</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_lwd &lt;- c(1.5, 1.5, 1.2, 1.2)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">325</td>
+                    <td class="num">44</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">#' @importFrom survival survfit Surv coxph</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">326</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">45</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_lty &lt;- use_line_types</pre>
+                      <pre class="language-r">#' @importFrom lmtest coeftest coefci</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">327</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">46</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_lwd &lt;- c(1.5, 1.5, 1.2, 1.2)</pre>
+                      <pre class="language-r">#' @importFrom sandwich vcovHC</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">328</td>
+                    <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' @importFrom boot boot boot.ci</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">329</td>
+                    <td class="num">48</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @return A list, contains 'descriptive' and 'inferential'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">330</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">49</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(use_colors)) {</pre>
+                      <pre class="language-r">#' @example inst/examples/maic_anchored_binary_ex.R</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">331</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">50</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_col &lt;- c("#5450E4", "#00857C", "#6ECEB2", "#7B68EE")</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">332</td>
+                    <td class="num">51</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">333</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">52</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_col &lt;- use_colors</pre>
+                      <pre class="language-r">maic_anchored &lt;- function(weights_object,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">334</td>
+                    <td class="num">53</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">                          ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">335</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">54</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_col2 &lt;- col2rgb(use_col) # preparing semi-transparent colors</pre>
+                      <pre class="language-r">                          pseudo_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">336</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">55</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_col2 &lt;- rgb(use_col2[1, ], use_col2[2, ], use_col2[3, ], alpha = use_pch_alpha, maxColorValue = 255)</pre>
+                      <pre class="language-r">                          trt_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">337</td>
+                    <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                          trt_agd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">338</td>
+                    <td class="num">57</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ## : first subplot: KM curve -------------------</pre>
+                      <pre class="language-r">                          trt_common,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">339</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # base plot</pre>
+                      <pre class="language-r">                          trt_var_ipd = "ARM",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">340</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">59</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  par(bty = "n", tcl = -0.15, mgp = c(1.8, 0.4, 0), cex.lab = 0.85, cex.axis = 0.8, cex.main = 0.9, mar = c(3, 4, 5, 1))</pre>
+                      <pre class="language-r">                          trt_var_agd = "ARM",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">341</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">60</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  plot(0, 0,</pre>
+                      <pre class="language-r">                          endpoint_type = "tte",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">342</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">61</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    type = "n", xlab = paste0("Time in ", time_scale), ylab = "Survival Probability",</pre>
+                      <pre class="language-r">                          endpoint_name = "Time to Event Endpoint",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">343</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">62</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ylim = c(0, 1), xlim = t_range, yaxt = "n", xaxt = "n",</pre>
+                      <pre class="language-r">                          eff_measure = c("HR", "OR", "RR", "RD"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">344</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">63</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    main = paste0(main_title, "\nEndpoint:", endpoint_name)</pre>
+                      <pre class="language-r">                          boot_ci_type = c("norm", "basic", "stud", "perc", "bca"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">345</td>
+                    <td class="num">64</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">                          # time to event specific args</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">346</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">65</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  axis(2, las = 1)</pre>
+                      <pre class="language-r">                          time_scale = "months",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">347</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">66</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!is.null(time_grid)) {</pre>
+                      <pre class="language-r">                          km_conf_type = "log-log",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">348</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">67</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    axis(1, at = time_grid)</pre>
+                      <pre class="language-r">                          # binary specific args</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">349</td>
+                    <td class="num">68</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">                          binary_robust_cov_type = "HC3") {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">350</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">69</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    axis(1)</pre>
+                      <pre class="language-r">  # ==&gt; Initial Setup ------------------------------------------</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">351</td>
+                    <td class="num">70</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  # ~~~ Create the hull for the output from this function</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">352</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">71</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  res &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">353</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">72</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # add km line</pre>
+                      <pre class="language-r">    descriptive = list(),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">354</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">73</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  for (ii in 1:nlevels(kmdat$treatment)) {</pre>
+                      <pre class="language-r">    inferential = list()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">355</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">74</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    tmpkmdat &lt;- kmdat[as.numeric(kmdat$treatment) == ii, , drop = FALSE]</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">356</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">75</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    lines(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">357</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">76</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      y = tmpkmdat$surv,</pre>
+                      <pre class="language-r">  res_AB &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">358</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">77</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      x = get_time_as(tmpkmdat$time, time_scale),</pre>
+                      <pre class="language-r">    est = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">359</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">78</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      col = use_col[ii],</pre>
+                      <pre class="language-r">    se = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">360</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">79</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      lty = use_lty[ii],</pre>
+                      <pre class="language-r">    ci_l = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">361</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">80</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      lwd = use_lwd[ii],</pre>
+                      <pre class="language-r">    ci_u = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">362</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">81</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      type = "s"</pre>
+                      <pre class="language-r">    pval = NA</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">363</td>
+                    <td class="num">82</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">364</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">83</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    tmpid &lt;- (tmpkmdat$censor != 0) # cannot just ==1, anticipating weighted case</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">365</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">84</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    points(</pre>
+                      <pre class="language-r">  # ~~~ Initial colname process and precheck on effect measure</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">366</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">85</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      y = tmpkmdat$surv[tmpid],</pre>
+                      <pre class="language-r">  names(ipd) &lt;- toupper(names(ipd))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">367</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">86</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      x = get_time_as(tmpkmdat$time[tmpid], time_scale),</pre>
+                      <pre class="language-r">  names(pseudo_ipd) &lt;- toupper(names(pseudo_ipd))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">368</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">87</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      col = use_col2[ii],</pre>
+                      <pre class="language-r">  trt_var_ipd &lt;- toupper(trt_var_ipd)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">369</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">88</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pch = 3,</pre>
+                      <pre class="language-r">  trt_var_agd &lt;- toupper(trt_var_agd)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">370</td>
+                    <td class="num">89</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      cex = use_pch_cex</pre>
+                      <pre class="language-r">  if (length(eff_measure) &gt; 1) eff_measure &lt;- NULL</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">371</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">90</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  if (is.null(eff_measure)) eff_measure &lt;- list(binary = "OR", tte = "HR")[[endpoint_type]]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">372</td>
+                    <td class="num">91</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">373</td>
+                    <td class="num">92</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # ~~~ Setup ARM column and make related pre-checks</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">374</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">93</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ## : second subplot: risk set table (if applicable) -------------------</pre>
+                      <pre class="language-r">  if (!trt_var_ipd %in% names(ipd)) stop("cannot find arm indicator column trt_var_ipd in ipd")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">375</td>
+                    <td class="num">94</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (show_risk_set) {</pre>
+                      <pre class="language-r">  if (!trt_var_agd %in% names(pseudo_ipd)) stop("cannot find arm indicator column trt_var_agd in pseudo_ipd")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">376</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">95</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # add legend, with treatment index</pre>
+                      <pre class="language-r">  if (trt_var_ipd != "ARM") ipd$ARM &lt;- ipd[[trt_var_ipd]]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">377</td>
+                    <td class="num">96</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    legend("topright",</pre>
+                      <pre class="language-r">  if (trt_var_agd != "ARM") pseudo_ipd$ARM &lt;- pseudo_ipd[[trt_var_agd]]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">378</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">97</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      bty = "n",</pre>
+                      <pre class="language-r">  ipd$ARM &lt;- as.character(ipd$ARM) # just to avoid potential error when merging</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">379</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">98</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      cex = 0.8,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">380</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">99</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      lty = use_lty[1:nlevels(kmdat$treatment)],</pre>
+                      <pre class="language-r">  # ~~~ More pre-checks</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">381</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">100</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      lwd = use_lwd[1:nlevels(kmdat$treatment)],</pre>
+                      <pre class="language-r">  pseudo_ipd$ARM &lt;- as.character(pseudo_ipd$ARM) # just to avoid potential error when merging</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">382</td>
+                    <td class="num">101</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      col = use_col[1:nlevels(kmdat$treatment)],</pre>
+                      <pre class="language-r">  if (!trt_ipd %in% ipd$ARM) stop("trt_ipd does not exist in ipd$ARM")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">383</td>
+                    <td class="num">102</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      legend = paste0("(T", 1:nlevels(kmdat$treatment), ") ", levels(kmdat$treatment))</pre>
+                      <pre class="language-r">  if (!trt_agd %in% pseudo_ipd$ARM) stop("trt_agd does not exist in pseudo_ipd$ARM")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">384</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">103</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  if (!trt_common %in% ipd$ARM) stop("trt_common does not exist in ipd$ARM")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">385</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">104</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  if (!trt_common %in% pseudo_ipd$ARM) stop("trt_common does not exist in pseudo_ipd$ARM")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">386</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">105</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # add risk set table</pre>
+                      <pre class="language-r">  ipd_arms &lt;- unique(ipd$ARM)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">387</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">106</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    par(bty = "n", tcl = -0.15, mgp = c(1.8, 0.4, 0), mar = c(1, 4, 0, 1))</pre>
+                      <pre class="language-r">  pseudo_ipd_arms &lt;- unique(pseudo_ipd$ARM)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">388</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">107</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    plot(0, 0,</pre>
+                      <pre class="language-r">  if (!length(ipd_arms) &gt;= 2) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">389</td>
+                    <td class="num">108</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      type = "n", xlab = "", ylab = "", main = NULL,</pre>
+                      <pre class="language-r">    stop("In anchored case, there should be at least two arms in ipd, but you have: ", toString(ipd_arms))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">390</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">109</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ylim = c(nlevels(kmdat$treatment) + 1.2, -0.5),</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">391</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">110</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      xlim = t_range,</pre>
+                      <pre class="language-r">  if (!length(pseudo_ipd_arms) &gt;= 2) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">392</td>
+                    <td class="num">111</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      yaxt = "n", xaxt = "n"</pre>
+                      <pre class="language-r">    stop("In anchored case, there should be at least two arms in pseudo_ipd, but you have: ", toString(pseudo_ipd_arms))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">393</td>
+                    <td class="num">112</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">394</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">113</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    axis(2,</pre>
+                      <pre class="language-r">  endpoint_type &lt;- match.arg(endpoint_type, c("binary", "tte"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">395</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">114</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      at = 1:nlevels(kmdat$treatment), labels = paste0("T", 1:nlevels(kmdat$treatment)),</pre>
+                      <pre class="language-r">  if (!"maicplus_estimate_weights" %in% class(weights_object)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">396</td>
+                    <td class="num">115</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      line = NA, lty = "blank", las = 1</pre>
+                      <pre class="language-r">    stop("weights_object should be an object returned by estimate_weights")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">397</td>
+                    <td class="num">116</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">398</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">117</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  if (any(duplicated(ipd$USUBJID))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">399</td>
+                    <td class="num">118</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    for (ii in 1:nlevels(kmdat$treatment)) {</pre>
+                      <pre class="language-r">    warning(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">400</td>
+                    <td class="num">119</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tmpkmdat &lt;- kmdat[as.numeric(kmdat$treatment) == ii, , drop = FALSE]</pre>
+                      <pre class="language-r">      "check your ipd, it has duplicated usubjid, this indicates, ",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">401</td>
+                    <td class="num">120</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tmptime &lt;- get_time_as(tmpkmdat$time, time_scale)</pre>
+                      <pre class="language-r">      "it might contain multiple endpoints for each subject"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">402</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">121</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tmpnr &lt;- sapply(time_grid, function(kk) {</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">403</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">122</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        tmpid &lt;- which(tmptime &gt; kk)</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">404</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">123</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (length(tmpid) == 0) {</pre>
+                      <pre class="language-r">  if (!all(ipd$USUBJID %in% weights_object$data$USUBJID)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">405</td>
+                    <td class="num">124</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          if (min(tmpkmdat$n.risk) == 0) {</pre>
+                      <pre class="language-r">    stop(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">406</td>
+                    <td class="num">125</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            tmpid &lt;- which.min(tmpkmdat$n.risk)[1]</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">407</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">          } else {</pre>
+                      <pre class="language-r">      "These patients in ipd cannot be found in weights_object ",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">408</td>
+                    <td class="num">126</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            tmpid &lt;- NULL</pre>
+                      <pre class="language-r">      toString(setdiff(ipd$USUBJID, weights_object$USUBJID))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">409</td>
+                    <td class="num">127</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          }</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">410</td>
+                    <td class="num">128</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">411</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">129</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        tout &lt;- ifelse(is.null(tmpid), "n/a", round(tmpkmdat$n.risk[tmpid], 1))</pre>
+                      <pre class="language-r">  time_scale &lt;- match.arg(arg = time_scale, choices = c("days", "weeks", "months", "years"))</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">130</td>
+                    <td class="coverage">3<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (endpoint_type == "binary") { # for binary effect measure</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">412</td>
+                    <td class="num">131</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      })</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">413</td>
+                    <td class="num">132</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      text(0, 0, labels = "Number at risk", pos = 4, cex = 0.8, offset = -0.8)</pre>
+                      <pre class="language-r">    if (any(!c("USUBJID", "RESPONSE") %in% names(ipd))) stop("ipd should have 'USUBJID', 'RESPONSE' columns at minimum")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">414</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">133</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      text(</pre>
+                      <pre class="language-r">    eff_measure &lt;- match.arg(eff_measure, choices = c("OR", "RD", "RR"), several.ok = FALSE)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">415</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">134</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        y = rep(ii, length(time_grid)),</pre>
+                      <pre class="language-r">  } else if (endpoint_type == "tte") { # for time to event effect measure</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">416</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">135</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        x = time_grid,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">417</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">136</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        labels = tmpnr,</pre>
+                      <pre class="language-r">    if (!all(c("USUBJID", "TIME", "EVENT", trt_var_ipd) %in% names(ipd))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">418</td>
+                    <td class="num">137</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        col = use_col[ii],</pre>
+                      <pre class="language-r">      stop("ipd needs to include at least USUBJID, TIME, EVENT, ", toString(trt_var_ipd))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">138</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    }</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">139</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    if (!all(c("TIME", "EVENT", trt_var_agd) %in% names(pseudo_ipd))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">419</td>
+                    <td class="num">140</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        cex = 0.75</pre>
+                      <pre class="language-r">      stop("pseudo_ipd needs to include at least TIME, EVENT, ", toString(trt_var_agd))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">420</td>
+                    <td class="num">141</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">421</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">142</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      text(0, nlevels(kmdat$treatment) + 1,</pre>
+                      <pre class="language-r">    eff_measure &lt;- match.arg(eff_measure, choices = c("HR"), several.ok = FALSE)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">422</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">143</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        pos = 4, cex = 0.7, offset = -0.8, col = "gray30",</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">423</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">144</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        labels = "Note: Number at risk for adjusted/weighted treament arm is the sum of individual weight at risk."</pre>
+                      <pre class="language-r">  boot_ci_type &lt;- match.arg(boot_ci_type)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">424</td>
+                    <td class="num">145</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">425</td>
+                    <td class="num">146</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">  # ==&gt; IPD and AgD data preparation ------------------------------------------</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">426</td>
+                    <td class="num">147</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">  # : subset ipd, retain only ipd from interested trts</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">148</td>
+                    <td class="coverage">3<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  ipd &lt;- ipd[ipd$ARM %in% c(trt_ipd, trt_common), , drop = TRUE]</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">149</td>
+                    <td class="coverage">3<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  pseudo_ipd &lt;- pseudo_ipd[pseudo_ipd$ARM %in% c(trt_agd, trt_common), , drop = TRUE]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">427</td>
+                    <td class="num">150</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # add simple</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">428</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">151</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    legend("topright",</pre>
+                      <pre class="language-r">  # : assign weights to real and pseudo ipd</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">429</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">152</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      bty = "n",</pre>
+                      <pre class="language-r">  ipd$weights &lt;- weights_object$data$weights[match(weights_object$data$USUBJID, ipd$USUBJID)]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">430</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">153</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      cex = 0.8,</pre>
+                      <pre class="language-r">  pseudo_ipd$weights &lt;- 1</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">154</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (!"USUBJID" %in% names(pseudo_ipd)) pseudo_ipd$USUBJID &lt;- paste0("ID", seq_len(nrow(pseudo_ipd)))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">155</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">156</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # : give warning when individual pts in IPD has no weights</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">157</td>
+                    <td class="coverage">3<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (any(is.na(ipd$weights))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">431</td>
+                    <td class="num">158</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      lty = use_lty[1:nlevels(kmdat$treatment)],</pre>
+                      <pre class="language-r">    ipd &lt;- ipd[!is.na(ipd$weights), , drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">432</td>
+                    <td class="num">159</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      lwd = use_lwd[1:nlevels(kmdat$treatment)],</pre>
+                      <pre class="language-r">    warning(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">433</td>
+                    <td class="num">160</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      col = use_col[1:nlevels(kmdat$treatment)],</pre>
+                      <pre class="language-r">      "These USUBJID in IPD have no weight in weights_object and hence excluded from analysis: ",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">434</td>
+                    <td class="num">161</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      legend = levels(kmdat$treatment)</pre>
+                      <pre class="language-r">      toString(ipd$USUBJID[is.na(ipd$weights)])</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">435</td>
+                    <td class="num">162</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">436</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">163</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    if (nrow(ipd) == 0) stop("There are no patients with valid weights in IPD!")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">437</td>
+                    <td class="num">164</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">438</td>
+                    <td class="num">165</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">439</td>
+                    <td class="num">166</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # : retain necessary columns</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">440</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">167</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Diagnosis plot of proportional hazard assumption for anchored and unanchored</pre>
+                      <pre class="language-r">  outcome_cols &lt;- if (endpoint_type == "tte") c("TIME", "EVENT") else "RESPONSE"</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">441</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">168</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  retain_cols &lt;- c("USUBJID", "ARM", outcome_cols, "weights")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">442</td>
+                    <td class="num">169</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param weights_object an object returned by \code{estimate_weight}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">443</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">170</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param tte_ipd a data frame of individual patient data (IPD) of internal trial, contain at least "USUBJID", "EVENT",</pre>
+                      <pre class="language-r">  ipd &lt;- ipd[, retain_cols, drop = FALSE]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">444</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">171</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "TIME" columns and a column indicating treatment assignment</pre>
+                      <pre class="language-r">  pseudo_ipd &lt;- pseudo_ipd[, retain_cols, drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">445</td>
+                    <td class="num">172</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param tte_pseudo_ipd a data frame of pseudo IPD by digitized KM curves of external trial (for time-to-event</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">446</td>
+                    <td class="num">173</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   endpoint), contain at least "EVENT", "TIME"</pre>
+                      <pre class="language-r">  # : merge real and pseudo ipds, only used if apply contrast method,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">447</td>
+                    <td class="num">174</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_ipd  a string, name of the interested investigation arm in internal trial \code{dat_igd} (real IPD)</pre>
+                      <pre class="language-r">  #   since contrast method is not implemented in v0.1, this R obj is not used</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">448</td>
+                    <td class="num">175</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_agd a string, name of the interested investigation arm in external trial \code{dat_pseudo} (pseudo IPD)</pre>
+                      <pre class="language-r">  #   just a placeholder</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">449</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">176</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_common a string, name of the common comparator in internal and external trial, by default is NULL,</pre>
+                      <pre class="language-r">  dat &lt;- rbind(ipd, pseudo_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">450</td>
+                    <td class="num">177</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   indicating unanchored case</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">451</td>
+                    <td class="num">178</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_var_ipd a string, column name in \code{dat_ipd} that contains the treatment assignment</pre>
+                      <pre class="language-r">  # : setup ARM column as a factor,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">452</td>
+                    <td class="num">179</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_var_agd a string, column name in \code{dat_ipd} that contains the treatment assignment</pre>
+                      <pre class="language-r">  # * these line cannot be move prior to "dat &lt;- rbind(ipd, pseudo_ipd)"</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">453</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">180</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param endpoint_name a string, name of time to event endpoint, to be show in the last line of title</pre>
+                      <pre class="language-r">  ipd$ARM &lt;- factor(ipd$ARM, levels = c(trt_common, trt_ipd))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">454</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">181</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param time_scale a string, time unit of median survival time, taking a value of 'years', 'months', 'weeks' or 'days'</pre>
+                      <pre class="language-r">  pseudo_ipd$ARM &lt;- factor(pseudo_ipd$ARM, levels = c(trt_common, trt_agd))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">455</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">182</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param zph_transform a string, pass to \code{survival::cox.zph}, default is "log"</pre>
+                      <pre class="language-r">  dat$ARM &lt;- factor(dat$ARM, levels = c(trt_common, trt_agd, trt_ipd))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">456</td>
+                    <td class="num">183</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param zph_log_hazard a logical, if TRUE (default), y axis of the time dependent hazard function is log-hazard,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">457</td>
+                    <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   otherwise, hazard.</pre>
+                      <pre class="language-r">  # ==&gt; Inferential output ------------------------------------------</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">458</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">185</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  result &lt;- if (endpoint_type == "tte") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">459</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">186</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a 3 by 2 plot, include log-cumulative hazard plot, time dependent hazard function and unscaled Schoenfeld</pre>
+                      <pre class="language-r">    maic_anchored_tte(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">460</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">187</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   residual plot, before and after matching</pre>
+                      <pre class="language-r">      res,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">461</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">188</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      res_BC = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">462</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">189</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ph_diagplot &lt;- function(weights_object,</pre>
+                      <pre class="language-r">      ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">463</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">190</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        tte_ipd,</pre>
+                      <pre class="language-r">      pseudo_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">464</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">191</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        tte_pseudo_ipd,</pre>
+                      <pre class="language-r">      km_conf_type,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">465</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">192</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        trt_ipd,</pre>
+                      <pre class="language-r">      time_scale,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">466</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">193</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        trt_agd,</pre>
+                      <pre class="language-r">      weights_object,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">467</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">194</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        trt_common = NULL,</pre>
+                      <pre class="language-r">      endpoint_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">468</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">195</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        trt_var_ipd = "ARM",</pre>
+                      <pre class="language-r">      trt_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">469</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">196</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        trt_var_agd = "ARM",</pre>
+                      <pre class="language-r">      trt_agd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">470</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">197</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        endpoint_name = "Time to Event Endpoint",</pre>
+                      <pre class="language-r">      boot_ci_type</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">471</td>
+                    <td class="num">198</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        time_scale,</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">472</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">199</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        zph_transform = "log",</pre>
+                      <pre class="language-r">  } else if (endpoint_type == "binary") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">473</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">200</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                        zph_log_hazard = TRUE) {</pre>
+                      <pre class="language-r">    maic_anchored_binary(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">474</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">201</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(tte_ipd) &lt;- toupper(names(tte_ipd))</pre>
+                      <pre class="language-r">      res,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">475</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">202</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(tte_pseudo_ipd) &lt;- toupper(names(tte_pseudo_ipd))</pre>
+                      <pre class="language-r">      res_BC = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">476</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">203</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  trt_var_ipd &lt;- toupper(trt_var_ipd)</pre>
+                      <pre class="language-r">      ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">477</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">204</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  trt_var_agd &lt;- toupper(trt_var_agd)</pre>
+                      <pre class="language-r">      pseudo_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">478</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">205</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      binary_robust_cov_type,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">479</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">206</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # pre check</pre>
+                      <pre class="language-r">      weights_object,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">480</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">207</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!"maicplus_estimate_weights" %in% class(weights_object)) {</pre>
+                      <pre class="language-r">      endpoint_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">481</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">208</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("weights_object should be an object returned by estimate_weights")</pre>
+                      <pre class="language-r">      eff_measure,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">482</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">209</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">      trt_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">483</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">210</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!all(c("USUBJID", "TIME", "EVENT", trt_var_ipd) %in% names(tte_ipd))) {</pre>
+                      <pre class="language-r">      trt_agd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">484</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">211</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("tte_ipd needs to include at least USUBJID, TIME, EVENT, ", trt_var_ipd)</pre>
+                      <pre class="language-r">      boot_ci_type</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">485</td>
+                    <td class="num">212</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">486</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">213</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!all(c("TIME", "EVENT", trt_var_agd) %in% names(tte_pseudo_ipd))) {</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">487</td>
+                    <td class="num">214</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("tte_ipd needs to include at least TIME, EVENT, ", trt_var_agd)</pre>
+                      <pre class="language-r">    stop("Endpoint type ", endpoint_type, " currently unsupported.")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">488</td>
+                    <td class="num">215</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">489</td>
+                    <td class="num">216</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">490</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">217</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # preparing analysis data</pre>
+                      <pre class="language-r">  result</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">491</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">218</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  is_anchored &lt;- ifelse(is.null(trt_common), FALSE, TRUE)</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">492</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">219</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_ipd &lt;- tte_ipd[tte_ipd[[trt_var_ipd]] %in% c(trt_ipd, trt_common), , drop = TRUE]</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">493</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">220</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_pseudo_ipd &lt;- tte_pseudo_ipd[tte_pseudo_ipd[[trt_var_agd]] %in% c(trt_agd, trt_common), , drop = TRUE]</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">494</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">221</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_ipd$weights &lt;- weights_object$data$weights[match(weights_object$data$USUBJID, tte_ipd$USUBJID)]</pre>
+                      <pre class="language-r"># MAIC inference functions for TTE outcome type ------------</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">495</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">222</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_pseudo_ipd$weights &lt;- 1</pre>
+                      <pre class="language-r">maic_anchored_tte &lt;- function(res,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">496</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">223</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_ipd$TIME2 &lt;- get_time_as(tte_ipd$TIME, as = time_scale) # for cox.zph</pre>
+                      <pre class="language-r">                              res_BC = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">497</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">224</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_pseudo_ipd$TIME2 &lt;- get_time_as(tte_pseudo_ipd$TIME, as = time_scale) # for cox.zph</pre>
+                      <pre class="language-r">                              ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">498</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">225</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!"USUBJID" %in% names(tte_pseudo_ipd)) tte_pseudo_ipd$USUBJID &lt;- paste0("ID", seq_len(nrow(tte_pseudo_ipd)))</pre>
+                      <pre class="language-r">                              pseudo_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">499</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">226</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (trt_var_ipd != "ARM") tte_ipd$ARM &lt;- tte_ipd[[trt_var_ipd]]</pre>
+                      <pre class="language-r">                              km_conf_type,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">500</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">227</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (trt_var_agd != "ARM") tte_pseudo_ipd$ARM &lt;- tte_pseudo_ipd[[trt_var_agd]]</pre>
+                      <pre class="language-r">                              time_scale,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">501</td>
+                    <td class="num">228</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                              weights_object,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">502</td>
+                    <td class="num">229</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # prepare plot data</pre>
+                      <pre class="language-r">                              endpoint_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">503</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">230</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  retain_cols &lt;- c("USUBJID", "TIME", "TIME2", "EVENT", "ARM", "weights")</pre>
+                      <pre class="language-r">                              trt_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">504</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">231</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!is_anchored) {</pre>
+                      <pre class="language-r">                              trt_agd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">505</td>
+                    <td class="num">232</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # unanchored case</pre>
+                      <pre class="language-r">                              boot_ci_type) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">506</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">233</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    tte_dat &lt;- rbind(</pre>
+                      <pre class="language-r">  # Analysis table (Cox model) before and after matching, incl Median Survival Time</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">507</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">234</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tte_ipd[, retain_cols, drop = FALSE],</pre>
+                      <pre class="language-r">  # derive km w and w/o weights</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">508</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">235</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tte_pseudo_ipd[, retain_cols, drop = FALSE]</pre>
+                      <pre class="language-r">  kmobj_ipd &lt;- survfit(Surv(TIME, EVENT) ~ ARM, ipd, conf.type = km_conf_type)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">509</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">236</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  kmobj_ipd_adj &lt;- survfit(Surv(TIME, EVENT) ~ ARM, ipd, weights = ipd$weights, conf.type = km_conf_type)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">510</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">237</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">  kmobj_agd &lt;- survfit(Surv(TIME, EVENT) ~ ARM, pseudo_ipd, conf.type = km_conf_type)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">511</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">238</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    tte_dat &lt;- tte_ipd[, retain_cols, drop = FALSE]</pre>
+                      <pre class="language-r">  res$descriptive[["survfit_ipd_before"]] &lt;- survfit_makeup(kmobj_ipd)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">512</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">239</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  res$descriptive[["survfit_ipd_after"]] &lt;- survfit_makeup(kmobj_ipd_adj)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">513</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">240</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  kmobj &lt;- survival::survfit(Surv(TIME, EVENT) ~ ARM, tte_dat, conf.type = "log-log")</pre>
+                      <pre class="language-r">  res$descriptive[["survfit_pseudo"]] &lt;- survfit_makeup(kmobj_agd)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">514</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">241</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  kmobj_adj &lt;- survival::survfit(Surv(TIME, EVENT) ~ ARM, tte_dat, conf.type = "log-log", weights = weights)</pre>
+                      <pre class="language-r">  # derive median survival time</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">515</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">242</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  coxobj &lt;- survival::coxph(Surv(TIME, EVENT) ~ ARM, data = tte_dat)</pre>
+                      <pre class="language-r">  medSurv_ipd &lt;- medSurv_makeup(kmobj_ipd, legend = "IPD, before matching", time_scale = time_scale)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">516</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">243</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  coxobj2 &lt;- survival::coxph(Surv(TIME2, EVENT) ~ ARM, data = tte_dat)</pre>
+                      <pre class="language-r">  medSurv_ipd_adj &lt;- medSurv_makeup(kmobj_ipd_adj, legend = "IPD, after matching", time_scale = time_scale)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">517</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">244</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  zphobj &lt;- survival::cox.zph(coxobj2, transform = zph_transform, global = FALSE)</pre>
+                      <pre class="language-r">  medSurv_agd &lt;- medSurv_makeup(kmobj_agd, legend = "AgD, external", time_scale = time_scale)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">518</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">245</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  coxobj_adj &lt;- survival::coxph(Surv(TIME, EVENT) ~ ARM, data = tte_dat, weights = weights)</pre>
+                      <pre class="language-r">  medSurv_out &lt;- rbind(medSurv_ipd, medSurv_ipd_adj, medSurv_agd)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">519</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">246</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  coxobj_adj2 &lt;- survival::coxph(Surv(TIME2, EVENT) ~ ARM, data = tte_dat, weights = weights)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">520</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">247</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  zphobj_adj &lt;- survival::cox.zph(coxobj_adj2, transform = zph_transform, global = FALSE)</pre>
+                      <pre class="language-r">  res$inferential[["report_median_surv"]] &lt;- medSurv_out</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">521</td>
+                    <td class="num">248</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">522</td>
+                    <td class="num">249</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # making the plot</pre>
+                      <pre class="language-r">  # ~~~ Analysis table (Cox model) before and after matching</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">523</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">250</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
+                      <pre class="language-r">  # fit PH Cox regression model</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">524</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">251</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  par(mfrow = c(3, 2), cex.lab = 0.85, cex.axis = 0.8, cex.main = 0.9)</pre>
+                      <pre class="language-r">  coxobj_ipd &lt;- coxph(Surv(TIME, EVENT) ~ ARM, ipd) # robust = TRUE or not makes a diff</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">525</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">252</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  on.exit(par(original_par))</pre>
+                      <pre class="language-r">  coxobj_ipd_adj &lt;- coxph(Surv(TIME, EVENT) ~ ARM, ipd, weights = weights, robust = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">526</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  # log-cum-hazard plot</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">527</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">253</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ph_diagplot_lch(kmobj,</pre>
+                      <pre class="language-r">  coxobj_agd &lt;- coxph(Surv(TIME, EVENT) ~ ARM, pseudo_ipd)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">528</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">254</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    time_scale = time_scale,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">529</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">255</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    log_time = TRUE,</pre>
+                      <pre class="language-r">  res$inferential[["ipd_model_before"]] &lt;- coxobj_ipd</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">530</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">256</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    endpoint_name = endpoint_name,</pre>
+                      <pre class="language-r">  res$inferential[["ipd_model_after"]] &lt;- coxobj_ipd_adj</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">531</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">257</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    subtitle = "(Before Matching)"</pre>
+                      <pre class="language-r">  res$inferential[["agd_model"]] &lt;- coxobj_agd</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">532</td>
+                    <td class="num">258</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">533</td>
+                    <td class="num">259</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">534</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  ph_diagplot_lch(kmobj_adj,</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">535</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    time_scale = time_scale,</pre>
+                      <pre class="language-r">  # derive ipd exp arm vs agd exp arm via bucher</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">536</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">260</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    log_time = TRUE,</pre>
+                      <pre class="language-r">  res_AC &lt;- as.list(summary(coxobj_ipd_adj)$coef)[c(1, 4)] # est, robust se</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">537</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">261</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    endpoint_name = endpoint_name,</pre>
+                      <pre class="language-r">  if (is.null(res_BC)) res_BC &lt;- as.list(summary(coxobj_agd)$coef)[c(1, 3)] # est, se</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">538</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">262</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    subtitle = "(After Matching)"</pre>
+                      <pre class="language-r">  names(res_AC) &lt;- names(res_BC) &lt;- c("est", "se")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">539</td>
+                    <td class="num">263</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">540</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">264</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # time dependent hazard plot</pre>
+                      <pre class="language-r">  res_AB &lt;- bucher(res_AC, res_BC, conf_lv = 0.95)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">541</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">265</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  plot(zphobj,</pre>
+                      <pre class="language-r">  res_AB$est &lt;- exp(res_AB$est)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">542</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">266</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    main = paste0(</pre>
+                      <pre class="language-r">  res_AB$ci_l &lt;- exp(res_AB$ci_l)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">543</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">267</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "Time-dependent Hazard function (scaled Schoenfeld residual)\n",</pre>
+                      <pre class="language-r">  res_AB$ci_u &lt;- exp(res_AB$ci_u)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">544</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">268</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "Endpoint:", endpoint_name, "\n(Before Matching)"</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">545</td>
+                    <td class="num">269</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">  # : get bootstrapped estimates if applicable</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">546</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">270</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    resid = FALSE, se = TRUE, df = 4, nsmo = 40,</pre>
+                      <pre class="language-r">  if (!is.null(weights_object$boot)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">547</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">271</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # xlim = range(0,zphobj$time),</pre>
+                      <pre class="language-r">    keep_rows &lt;- setdiff(seq_len(nrow(weights_object$data)), weights_object$rows_with_missing)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">548</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">272</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ylab = ifelse(zph_log_hazard, "Log Hazard", "Hazard"),</pre>
+                      <pre class="language-r">    boot_ipd_id &lt;- weights_object$data[keep_rows, "USUBJID", drop = FALSE]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">549</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">273</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    xlab = paste("Time in", time_scale),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">550</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">274</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    lty = 1:2, lwd = 2, pch = 16, cex = 0.8,</pre>
+                      <pre class="language-r">    boot_ipd &lt;- merge(boot_ipd_id, ipd, by = "USUBJID", all.x = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">551</td>
+                    <td class="num">275</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    col = rgb(0, 0, 128, alpha = 120, maxColorValue = 255),</pre>
+                      <pre class="language-r">    if (nrow(boot_ipd) != nrow(boot_ipd_id)) stop("ipd has multiple observations for some patients")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">552</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">276</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    hr = (!zph_log_hazard), yaxt = "n"</pre>
+                      <pre class="language-r">    boot_ipd &lt;- boot_ipd[match(boot_ipd$USUBJID, boot_ipd_id$USUBJID), ]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">553</td>
+                    <td class="num">277</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">554</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  axis(2, las = 1)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">555</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">278</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pv &lt;- as.data.frame(zphobj$table)$p</pre>
+                      <pre class="language-r">    stat_fun &lt;- function(data, index, w_obj) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">556</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">279</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pv &lt;- ifelse(round(pv, 4) &lt; 0.0001, "&lt;0.0001", format(round(pv, 4), nsmall = 4))</pre>
+                      <pre class="language-r">      r &lt;- dynGet("r", ifnotfound = NA) # Get bootstrap iteration</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">557</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">280</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  legend("bottomright",</pre>
+                      <pre class="language-r">      if (!is.na(r)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">558</td>
+                    <td class="num">281</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    cex = 0.75, bty = "n", text.col = "dodgerblue3",</pre>
+                      <pre class="language-r">        if (!all(index == w_obj$boot[, 1, r])) stop("Bootstrap and weight indices don't match")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">559</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">282</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    legend = c(paste0("p-value: ", pv), paste0("time-transform: ", zph_transform)),</pre>
+                      <pre class="language-r">        boot_ipd &lt;- data[w_obj$boot[, 1, r], ]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">560</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">283</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    title = "PH test (survival::cox.zph)"</pre>
+                      <pre class="language-r">        boot_ipd$weights &lt;- w_obj$boot[, 2, r]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">561</td>
+                    <td class="num">284</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">562</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">285</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      boot_coxobj_dat_adj &lt;- coxph(Surv(TIME, EVENT) ~ ARM, boot_ipd, weights = boot_ipd$weights, robust = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">563</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  plot(zphobj_adj,</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">564</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">286</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    main = paste0(</pre>
+                      <pre class="language-r">      boot_res_AC &lt;- list(est = coef(boot_coxobj_dat_adj)[1], se = sqrt(vcov(boot_coxobj_dat_adj)[1, 1]))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">565</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">287</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "Time-dependent Hazard function (scaled Schoenfeld residual)\n",</pre>
+                      <pre class="language-r">      boot_res_AB &lt;- bucher(boot_res_AC, res_BC, conf_lv = 0.95)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">566</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">288</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "Endpoint:", endpoint_name, "\n(After Matching)"</pre>
+                      <pre class="language-r">      c(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">567</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">289</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">        est_AB = boot_res_AB$est,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">568</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">290</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    resid = FALSE, se = TRUE, df = 4, nsmo = 40,</pre>
+                      <pre class="language-r">        var_AB = boot_res_AB$se^2,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">569</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">291</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # xlim = range(0,zphobj$time),</pre>
+                      <pre class="language-r">        se_AB = boot_res_AB$se,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">570</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">292</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ylab = ifelse(zph_log_hazard, "Log Hazard", "Hazard"),</pre>
+                      <pre class="language-r">        est_AC = boot_res_AC$est,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">571</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">293</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    xlab = paste("Time in", time_scale),</pre>
+                      <pre class="language-r">        se_AC = boot_res_AC$se,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">572</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">294</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    lty = 1:2, lwd = 2, pch = 16, cex = 0.8,</pre>
+                      <pre class="language-r">        var_AC = boot_res_AC$se^2</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">573</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">295</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    col = rgb(0, 0, 128, alpha = 120, maxColorValue = 255),</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">574</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">296</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    hr = (!zph_log_hazard), yaxt = "n"</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">575</td>
+                    <td class="num">297</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">576</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">298</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  axis(2, las = 1)</pre>
+                      <pre class="language-r">    # Revert seed to how it was for weight bootstrap sampling</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">577</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">299</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pv &lt;- as.data.frame(zphobj_adj$table)$p</pre>
+                      <pre class="language-r">    old_seed &lt;- globalenv()$.Random.seed</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">578</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">300</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pv &lt;- ifelse(round(pv, 4) &lt; 0.0001, "&lt;0.0001", format(round(pv, 4), nsmall = 4))</pre>
+                      <pre class="language-r">    on.exit(suspendInterrupts(set_random_seed(old_seed)))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">579</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">301</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  legend("bottomright",</pre>
+                      <pre class="language-r">    set_random_seed(weights_object$boot_seed)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">580</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">302</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    cex = 0.75, bty = "n", text.col = "dodgerblue3",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">581</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">303</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    legend = c(paste0("p-value: ", pv), paste0("time-transform: ", zph_transform)),</pre>
+                      <pre class="language-r">    R &lt;- dim(weights_object$boot)[3]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">582</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">304</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    title = "PH test (survival::cox.zph)"</pre>
+                      <pre class="language-r">    boot_res &lt;- boot(boot_ipd, stat_fun, R = R, w_obj = weights_object, strata = weights_object$boot_strata)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">583</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">305</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">    boot_ci &lt;- boot.ci(boot_res, type = boot_ci_type, w_obj = weights_object)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">584</td>
+                    <td class="num">306</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">585</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">307</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # unscaled schoenfeld residual</pre>
+                      <pre class="language-r">    l_u_index &lt;- switch(boot_ci_type,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">586</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">308</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ph_diagplot_schoenfeld(coxobj,</pre>
+                      <pre class="language-r">      "norm" = list(2, 3, "normal"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">587</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">309</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    time_scale = time_scale,</pre>
+                      <pre class="language-r">      "basic" = list(4, 5, "basic"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">588</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">310</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    log_time = FALSE,</pre>
+                      <pre class="language-r">      "stud" = list(4, 5, "student"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">589</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">311</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    endpoint_name = endpoint_name,</pre>
+                      <pre class="language-r">      "perc" = list(4, 5, "percent"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">590</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">312</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    subtitle = "(Before Matching)"</pre>
+                      <pre class="language-r">      "bca" = list(4, 5, "bca")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">591</td>
+                    <td class="num">313</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">592</td>
+                    <td class="num">314</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">593</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">315</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ph_diagplot_schoenfeld(coxobj_adj,</pre>
+                      <pre class="language-r">    res$inferential[["boot_est"]] &lt;- boot_res</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">594</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">316</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    time_scale = time_scale,</pre>
+                      <pre class="language-r">    boot_res_AB &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">595</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">317</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    log_time = FALSE,</pre>
+                      <pre class="language-r">      est = exp(boot_res$t0[1]),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">596</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">318</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    endpoint_name = endpoint_name,</pre>
+                      <pre class="language-r">      se = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">597</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">319</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    subtitle = "(After Matching)"</pre>
+                      <pre class="language-r">      ci_l = exp(boot_ci[[l_u_index[[3]]]][l_u_index[[1]]]),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">598</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">320</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      ci_u = exp(boot_ci[[l_u_index[[3]]]][l_u_index[[2]]]),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">599</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">321</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      pval = NA</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">600</td>
+                    <td class="num">322</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">601</td>
+                    <td class="num">323</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' PH Diagnosis Plot of Log Cumulative Hazard Rate versus time or log-time</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">602</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">324</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    res$inferential[["boot_est"]] &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">603</td>
+                    <td class="num">325</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This plot is also known as log negative log survival rate.</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">604</td>
+                    <td class="num">326</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">605</td>
+                    <td class="num">327</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' a diagnosis plot for proportional hazard assumption, versus log-time (default) or time</pre>
+                      <pre class="language-r">  # : make analysis report table</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">606</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">328</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  res$inferential[["report_overall_robustCI"]] &lt;- rbind(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">607</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">329</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param km_fit returned object from \code{survival::survfit}</pre>
+                      <pre class="language-r">    report_table_tte(coxobj_ipd, medSurv_ipd, tag = paste0("IPD/", endpoint_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">608</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">330</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param time_scale a character string, 'years', 'months', 'weeks' or 'days', time unit of median survival time</pre>
+                      <pre class="language-r">    report_table_tte(coxobj_ipd_adj, medSurv_ipd_adj, tag = paste0("weighted IPD/", endpoint_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">609</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">331</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param log_time logical, TRUE (default) or FALSE</pre>
+                      <pre class="language-r">    report_table_tte(coxobj_agd, medSurv_agd, tag = paste0("Agd/", endpoint_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">610</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">332</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param endpoint_name a character string, name of the endpoint</pre>
+                      <pre class="language-r">    c(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">611</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">333</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param subtitle a character string, subtitle of the plot</pre>
+                      <pre class="language-r">      paste0("** adj.", trt_ipd, " vs ", trt_agd),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">612</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">334</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param exclude_censor logical, should censored data point be plotted</pre>
+                      <pre class="language-r">      rep("--", 4),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">613</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">335</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">      reformat(res_AB, pval_digits = 3)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">614</td>
+                    <td class="num">336</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' library(survival)</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">615</td>
+                    <td class="num">337</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' load(system.file("extdata", "combined_data_tte.rda", package = "maicplus", mustWork = TRUE))</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">616</td>
+                    <td class="num">338</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' kmobj &lt;- survfit(Surv(TIME, EVENT) ~ ARM, combined_data_tte, conf.type = "log-log")</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">617</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">339</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ph_diagplot_lch(kmobj,</pre>
+                      <pre class="language-r">  if (is.null(res$inferential[["boot_est"]])) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">618</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">340</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   time_scale = "month", log_time = TRUE,</pre>
+                      <pre class="language-r">    res$inferential[["report_overall_bootCI"]] &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">619</td>
+                    <td class="num">341</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   endpoint_name = "OS", subtitle = "(Before Matching)"</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">620</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">342</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">    temp_boot_res &lt;- boot_res_AB</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">621</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">343</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a plot of log cumulative hazard rate</pre>
+                      <pre class="language-r">    temp_boot_res$ci_l &lt;- boot_res_AB$ci_l</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">622</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">344</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">    temp_boot_res$ci_u &lt;- boot_res_AB$ci_u</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">623</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">345</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    class(temp_boot_res) &lt;- class(res_AB)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">624</td>
+                    <td class="num">346</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ph_diagplot_lch &lt;- function(km_fit,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">625</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">347</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            time_scale,</pre>
+                      <pre class="language-r">    res$inferential[["report_overall_bootCI"]] &lt;- rbind(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">626</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">348</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            log_time = TRUE,</pre>
+                      <pre class="language-r">      report_table_tte(coxobj_ipd, medSurv_ipd, tag = paste0("IPD/", endpoint_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">627</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">349</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            endpoint_name = "",</pre>
+                      <pre class="language-r">      report_table_tte(coxobj_ipd_adj, medSurv_ipd_adj, tag = paste0("weighted IPD/", endpoint_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">628</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">350</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            subtitle = "",</pre>
+                      <pre class="language-r">      report_table_tte(coxobj_agd, medSurv_agd, tag = paste0("AgD/", endpoint_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">629</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">351</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            exclude_censor = TRUE) {</pre>
+                      <pre class="language-r">      c(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">630</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">352</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  time_scale &lt;- match.arg(arg = time_scale, choices = c("days", "weeks", "months", "years"))</pre>
+                      <pre class="language-r">        paste0("** adj.", trt_ipd, " vs ", trt_agd),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">631</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">353</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        rep("--", 4),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">632</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">354</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  clldat &lt;- survfit_makeup(km_fit)</pre>
+                      <pre class="language-r">        reformat(boot_res_AB, pval_digits = 3)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">633</td>
+                    <td class="num">355</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">634</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (exclude_censor) {</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">635</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">356</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    clldat &lt;- lapply(clldat, function(xxt) xxt[xxt$censor == 0, , drop = FALSE])</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">636</td>
+                    <td class="num">357</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">637</td>
+                    <td class="num">358</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">638</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  all.times &lt;- get_time_as(do.call(rbind, clldat)$time, time_scale)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">639</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">359</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (log_time) all.times &lt;- log(all.times)</pre>
+                      <pre class="language-r">  # output</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">640</td>
+                    <td class="num">360</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  t_range &lt;- range(all.times)</pre>
+                      <pre class="language-r">  res</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">641</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">361</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  y_range &lt;- range(log(do.call(rbind, clldat)$cumhaz))</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">642</td>
+                    <td class="num">362</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">643</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">363</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
+                      <pre class="language-r"># MAIC inference functions for Binary outcome type ------------</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">644</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">364</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  par(mar = c(4, 4, 4, 1), bty = "n", tcl = -0.15, mgp = c(1.5, 0.3, 0))</pre>
+                      <pre class="language-r">maic_anchored_binary &lt;- function(res,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">645</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">365</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  on.exit(par(original_par))</pre>
+                      <pre class="language-r">                                 res_BC = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">646</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">366</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  plot(0, 0,</pre>
+                      <pre class="language-r">                                 ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">647</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">367</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    type = "n", xlab = paste0(ifelse(log_time, "Log-", ""), "Time in ", time_scale),</pre>
+                      <pre class="language-r">                                 pseudo_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">648</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">368</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ylab = "Log-Cumulative Hazard Rate",</pre>
+                      <pre class="language-r">                                 binary_robust_cov_type,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">649</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">369</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ylim = y_range, xlim = t_range, yaxt = "n",</pre>
+                      <pre class="language-r">                                 weights_object,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">650</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">370</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    main = paste0(</pre>
+                      <pre class="language-r">                                 endpoint_name,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">651</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">371</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "Log Cumulative Hazard versus Log Time\nEndpoint: ", endpoint_name,</pre>
+                      <pre class="language-r">                                 eff_measure,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">652</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">372</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ifelse(subtitle == "", "", "\n"), subtitle</pre>
+                      <pre class="language-r">                                 trt_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">653</td>
+                    <td class="num">373</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">                                 trt_agd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">654</td>
+                    <td class="num">374</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">                                 boot_ci_type) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">655</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">375</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  axis(2, las = 1)</pre>
+                      <pre class="language-r">  # ~~~ Analysis table</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">656</td>
+                    <td class="num">376</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # : set up proper link</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">657</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">377</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  trts &lt;- names(clldat)</pre>
+                      <pre class="language-r">  glm_link &lt;- switch(eff_measure,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">658</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">378</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  cols &lt;- c("dodgerblue3", "firebrick3")</pre>
+                      <pre class="language-r">    "RD" = poisson(link = "identity"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">659</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">379</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pchs &lt;- c(1, 4)</pre>
+                      <pre class="language-r">    "RR" = poisson(link = "log"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">660</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">380</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  for (i in seq_along(clldat)) {</pre>
+                      <pre class="language-r">    "OR" = binomial(link = "logit")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">661</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">381</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_x &lt;- get_time_as(clldat[[i]]$time, time_scale)</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">662</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">382</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (log_time) use_x &lt;- log(use_x)</pre>
+                      <pre class="language-r">  res_template &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">663</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">383</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    est = NA,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">664</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">384</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    lines(</pre>
+                      <pre class="language-r">    se = NA,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">665</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">385</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      y = log(clldat[[i]]$cumhaz),</pre>
+                      <pre class="language-r">    ci_l = NA,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">666</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">386</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      x = use_x, col = cols[i],</pre>
+                      <pre class="language-r">    ci_u = NA,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">667</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">387</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      type = "s",</pre>
+                      <pre class="language-r">    pval = NA</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">668</td>
+                    <td class="num">388</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">669</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">389</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    points(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">670</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">390</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      y = log(clldat[[i]]$cumhaz),</pre>
+                      <pre class="language-r">  # : fit glm for binary outcome and robust estimate with weights</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">671</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">391</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      x = use_x,</pre>
+                      <pre class="language-r">  binobj_ipd &lt;- glm(RESPONSE ~ ARM, ipd, family = glm_link)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">672</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">392</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      col = cols[i], pch = pchs[i], cex = 0.7</pre>
+                      <pre class="language-r">  binobj_ipd_adj &lt;- glm(RESPONSE ~ ARM, ipd, weights = weights, family = glm_link)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">673</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">393</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  binobj_agd &lt;- glm(RESPONSE ~ ARM, pseudo_ipd, family = glm_link)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">674</td>
+                    <td class="num">394</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">675</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">395</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  legend("bottomright",</pre>
+                      <pre class="language-r">  bin_robust_cov &lt;- sandwich::vcovHC(binobj_ipd_adj, type = binary_robust_cov_type)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">676</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">396</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bty = "n", lty = c(1, 1, 2), cex = 0.8,</pre>
+                      <pre class="language-r">  bin_robust_coef &lt;- lmtest::coeftest(binobj_ipd_adj, vcov. = bin_robust_cov)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">677</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">397</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    col = cols, pch = pchs, legend = paste0("Treatment: ", trts)</pre>
+                      <pre class="language-r">  bin_robust_ci &lt;- lmtest::coefci(binobj_ipd_adj, vcov. = bin_robust_cov)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">678</td>
+                    <td class="num">398</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">679</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">399</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  res$inferential[["ipd_model_before"]] &lt;- binobj_ipd</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">680</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">681</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">400</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  res$inferential[["ipd_model_after"]] &lt;- binobj_ipd_adj</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">682</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">401</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' PH Diagnosis Plot of Schoenfeld residuals for a Cox model fit</pre>
+                      <pre class="language-r">  res$inferential[["agd_model"]] &lt;- binobj_ipd</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">683</td>
+                    <td class="num">402</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">684</td>
+                    <td class="num">403</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param coxobj object returned from \code{\link[survival]{coxph}}</pre>
+                      <pre class="language-r">  # derive ipd exp arm vs agd exp arm via bucher</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">685</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">404</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param time_scale a character string, 'years', 'months', 'weeks' or 'days', time unit of median survival time</pre>
+                      <pre class="language-r">  res_AC &lt;- res_template</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">686</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">405</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param log_time logical, TRUE (default) or FALSE</pre>
+                      <pre class="language-r">  res_AC$est &lt;- bin_robust_coef[2, "Estimate"]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">687</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">406</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param endpoint_name a character string, name of the endpoint</pre>
+                      <pre class="language-r">  res_AC$se &lt;- bin_robust_coef[2, "Std. Error"]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">688</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">407</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param subtitle a character string, subtitle of the plot</pre>
+                      <pre class="language-r">  res_AC$ci_l &lt;- bin_robust_ci[2, "2.5 %"]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">689</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">408</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">  res_AC$ci_u &lt;- bin_robust_ci[2, "97.5 %"]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">690</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">409</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' library(survival)</pre>
+                      <pre class="language-r">  res_AC$pval &lt;- bin_robust_coef[2, "Pr(&gt;|z|)"]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">691</td>
+                    <td class="num">410</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' load(system.file("extdata", "combined_data_tte.rda", package = "maicplus", mustWork = TRUE))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">692</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">411</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' unweighted_cox &lt;- coxph(Surv(TIME, EVENT == 1) ~ ARM, data = combined_data_tte)</pre>
+                      <pre class="language-r">  if (is.null(res_BC)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">693</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">412</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ph_diagplot_schoenfeld(unweighted_cox,</pre>
+                      <pre class="language-r">    res_BC &lt;- list(est = coef(binobj_agd)[2], se = sqrt(vcov(binobj_agd)[2, 2]))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">694</td>
+                    <td class="num">413</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   time_scale = "month", log_time = TRUE,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">695</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">414</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   endpoint_name = "OS", subtitle = "(Before Matching)"</pre>
+                      <pre class="language-r">  res_AB &lt;- bucher(res_AC, res_BC, conf_lv = 0.95)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">696</td>
+                    <td class="num">415</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">697</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">416</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a plot of Schoenfeld residuals</pre>
+                      <pre class="language-r">  if (eff_measure %in% c("RR", "OR")) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">698</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">417</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">    res_AB$est &lt;- exp(res_AB$est)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">699</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">418</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    res_AB$se &lt;- sqrt((exp(res_AB$se^2) - 1) * exp(2 * res_AB$est + res_AB$se^2)) # log normal parameterization</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">700</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">419</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ph_diagplot_schoenfeld &lt;- function(coxobj,</pre>
+                      <pre class="language-r">    res_AB$ci_l &lt;- exp(res_AB$ci_l)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">701</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">420</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                   time_scale = "months",</pre>
+                      <pre class="language-r">    res_AB$ci_u &lt;- exp(res_AB$ci_u)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">702</td>
+                    <td class="num">421</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                   log_time = TRUE,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">703</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">422</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                   endpoint_name = "",</pre>
+                      <pre class="language-r">    res_AC$est &lt;- exp(res_AC$est)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">704</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">423</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                   subtitle = "") {</pre>
+                      <pre class="language-r">    res_AC$se &lt;- sqrt((exp(res_AC$se^2) - 1) * exp(2 * res_AC$est + res_AC$se^2)) # log normal parameterization</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">705</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">424</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # pre-check</pre>
+                      <pre class="language-r">    res_AC$ci_l &lt;- exp(res_AC$ci_l)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">706</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">425</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  time_scale &lt;- match.arg(arg = time_scale, choices = c("days", "weeks", "months", "years"))</pre>
+                      <pre class="language-r">    res_AC$ci_u &lt;- exp(res_AC$ci_u)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">707</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">426</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  } else if (eff_measure == "RD") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">708</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">427</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # prepare data</pre>
+                      <pre class="language-r">    res_AB$est &lt;- res_AB$est * 100</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">709</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">428</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  schresid &lt;- residuals(coxobj, type = "schoenfeld")</pre>
+                      <pre class="language-r">    res_AB$se &lt;- res_AB$se * 100</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">710</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">429</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  plot_x &lt;- get_time_as(as.numeric(names(schresid)), time_scale)</pre>
+                      <pre class="language-r">    res_AB$ci_l &lt;- res_AB$ci_l * 100</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">711</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">430</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (log_time) plot_x &lt;- log(plot_x)</pre>
+                      <pre class="language-r">    res_AB$ci_u &lt;- res_AB$ci_u * 100</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">712</td>
+                    <td class="num">431</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">713</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">432</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # loewss fit</pre>
+                      <pre class="language-r">    res_AC$est &lt;- res_AC$est * 100</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">714</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">433</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  fit0 &lt;- predict(loess(schresid ~ plot_x), se = TRUE)</pre>
+                      <pre class="language-r">    res_AC$se &lt;- res_AC$se * 100</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">715</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">434</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  uppband &lt;- fit0$fit + qt(0.975, fit0$df) * fit0$se</pre>
+                      <pre class="language-r">    res_AC$ci_l &lt;- res_AC$ci_l * 100</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">716</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">435</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  lowband &lt;- fit0$fit - qt(0.975, fit0$df) * fit0$se</pre>
+                      <pre class="language-r">    res_AC$ci_u &lt;- res_AC$ci_u * 100</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">717</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">436</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_yrange &lt;- range(schresid, uppband, lowband)</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">718</td>
+                    <td class="num">437</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">719</td>
+                    <td class="num">438</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # making the plot</pre>
+                      <pre class="language-r">  # : get bootstrapped estimates if applicable</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">720</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">439</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
+                      <pre class="language-r">  if (!is.null(weights_object$boot)) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">721</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">440</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  par(bty = "n", mar = c(4, 4, 4, 1), tcl = -0.15, mgp = c(1.5, 0.3, 0))</pre>
+                      <pre class="language-r">    keep_rows &lt;- setdiff(seq_len(nrow(weights_object$data)), weights_object$rows_with_missing)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">722</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">441</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  on.exit(par(original_par))</pre>
+                      <pre class="language-r">    boot_ipd_id &lt;- weights_object$data[keep_rows, "USUBJID", drop = FALSE]</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">723</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">442</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  plot(schresid ~ plot_x,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">724</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">443</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    type = "n",</pre>
+                      <pre class="language-r">    boot_ipd &lt;- merge(boot_ipd_id, ipd, by = "USUBJID", all.x = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">725</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">444</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    yaxt = "n", ylim = use_yrange,</pre>
+                      <pre class="language-r">    if (nrow(boot_ipd) != nrow(boot_ipd_id)) stop("ipd has multiple observations for some patients")</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">726</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">445</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ylab = "Unscaled Schoenfeld Residual",</pre>
+                      <pre class="language-r">    boot_ipd &lt;- boot_ipd[match(boot_ipd$USUBJID, boot_ipd_id$USUBJID), ]</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">727</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">446</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    xlab = paste0(ifelse(log_time, "Log-", ""), "Time in ", time_scale),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">728</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">447</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    main = paste0(</pre>
+                      <pre class="language-r">    stat_fun &lt;- function(data, index, w_obj, eff_measure) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">729</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">448</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "Unscaled Schoenfeld Residual\nEndpoint: ", endpoint_name,</pre>
+                      <pre class="language-r">      r &lt;- dynGet("r", ifnotfound = NA) # Get bootstrap iteration</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">730</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      ifelse(subtitle == "", "", "\n"), subtitle</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">731</td>
-                    <td class="coverage"></td>
+                    <td class="num">449</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">      if (!is.na(r)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">732</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">450</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">        if (!all(index == w_obj$boot[, 1, r])) stop("Bootstrap and weight indices don't match")</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">733</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">451</td>
+                    <td class="coverage">100<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  axis(2, las = 1)</pre>
+                      <pre class="language-r">        boot_ipd &lt;- data[w_obj$boot[, 1, r], ]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">734</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">452</td>
+                    <td class="coverage">100<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  lines(fit0$fit ~ plot_x, lty = 2, lwd = 1, col = rgb(0, 0, 128, 150, maxColorValue = 255))</pre>
+                      <pre class="language-r">        boot_ipd$weights &lt;- w_obj$boot[, 2, r]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">735</td>
+                    <td class="num">453</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # lines(uppband ~ plot_x, lty =2, lwd=1, col = rgb(0,0,128,120,maxColorValue = 255))</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">736</td>
+                    <td class="num">454</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # lines(lowband ~ plot_x, lty =2, lwd=1, col = rgb(0,0,128,120,maxColorValue = 255))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">737</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">455</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  polygon(</pre>
+                      <pre class="language-r">      boot_binobj_dat_adj &lt;- glm(RESPONSE ~ ARM, boot_ipd, weights = boot_ipd$weights, family = glm_link)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">738</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">456</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    x = c(plot_x, rev(plot_x)),</pre>
+                      <pre class="language-r">      boot_AC_est &lt;- coef(boot_binobj_dat_adj)[2]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">739</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">457</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    y = c(uppband, rev(lowband)),</pre>
+                      <pre class="language-r">      boot_AC_var &lt;- vcov(boot_binobj_dat_adj)[2, 2]</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">458</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">740</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">459</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    col = rgb(0, 0, 128, 60, maxColorValue = 255),</pre>
+                      <pre class="language-r">      boot_res_AC &lt;- list(est = boot_AC_est, se = sqrt(boot_AC_var))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">741</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">460</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    border = NA</pre>
+                      <pre class="language-r">      boot_res_AB &lt;- bucher(boot_res_AC, res_BC, conf_lv = 0.95)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">742</td>
+                    <td class="num">461</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">743</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">462</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  abline(h = 0, lty = 1, lwd = 1, col = "deeppink")</pre>
+                      <pre class="language-r">      c(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">744</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">463</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  points(schresid ~ plot_x,</pre>
+                      <pre class="language-r">        est_AB = boot_res_AB$est,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">745</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">464</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pch = 16,</pre>
+                      <pre class="language-r">        var_AB = boot_res_AB$se^2,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">746</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">465</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    cex = 0.85,</pre>
+                      <pre class="language-r">        se_AB = boot_res_AB$se,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">747</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">466</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    col = rgb(169, 169, 169, 120, maxColorValue = 255)</pre>
+                      <pre class="language-r">        est_AC = boot_res_AC$est,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">748</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">467</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">        se_AC = boot_res_AC$se,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">749</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">468</td>
+                    <td class="coverage">101<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">        var_AC = boot_res_AC$se^2</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/process_data.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">469</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># Functions for pre-processing data before conduct MAIC</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">2</td>
+                    <td class="num">470</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">471</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># Functions to be exported ---------------------------------------</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">472</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    # Revert seed to how it was for weight bootstrap sampling</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">5</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">473</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Pre-process aggregate data</pre>
+                      <pre class="language-r">    old_seed &lt;- globalenv()$.Random.seed</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">6</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">474</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    on.exit(suspendInterrupts(set_random_seed(old_seed)))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">475</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This function checks the format of the aggregate data.</pre>
+                      <pre class="language-r">    set_random_seed(weights_object$boot_seed)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">476</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Data is required to have three columns: STUDY, ARM, and N.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">9</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">477</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Column names that do not have legal suffixes (MEAN, MEDIAN, SD, COUNT, or PROP) are dropped.</pre>
+                      <pre class="language-r">    R &lt;- dim(weights_object$boot)[3]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">10</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">478</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' If a variable is a count variable, it is converted to proportions by dividing the sample size (N).</pre>
+                      <pre class="language-r">    boot_res &lt;- boot(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">11</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">479</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Note, when the count is specified, proportion is always calculated based on the count, that is,</pre>
+                      <pre class="language-r">      boot_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">480</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' specified proportion will be ignored if applicable.</pre>
+                      <pre class="language-r">      stat_fun,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">13</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">481</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' If the aggregated data comes from multiple sources (i.e. different analysis population) and</pre>
+                      <pre class="language-r">      R = R,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">14</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">482</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' sample size differs for each variable, one option is to specify proportion directly instead of count by using suffix</pre>
+                      <pre class="language-r">      w_obj = weights_object,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">15</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">483</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' _PROP.</pre>
+                      <pre class="language-r">      eff_measure = eff_measure,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">16</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">484</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      strata = weights_object$boot_strata</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">17</td>
+                    <td class="num">485</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param raw_agd raw aggregate data should contain STUDY, ARM, and N. Variable names should be followed</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">18</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">486</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' by legal suffixes (i.e. MEAN, MEDIAN, SD, COUNT, or PROP).</pre>
+                      <pre class="language-r">    boot_ci &lt;- boot.ci(boot_res, type = boot_ci_type, w_obj = weights_object)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">19</td>
+                    <td class="num">487</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">20</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">488</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">    l_u_index &lt;- switch(boot_ci_type,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">21</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">489</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' target_pop &lt;- read.csv(system.file("extdata", "aggregate_data_example_1.csv",</pre>
+                      <pre class="language-r">      "norm" = list(2, 3, "normal"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">22</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">490</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   package = "maicplus", mustWork = TRUE</pre>
+                      <pre class="language-r">      "basic" = list(4, 5, "basic"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">23</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">491</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ))</pre>
+                      <pre class="language-r">      "stud" = list(4, 5, "student"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">24</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">492</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' target_pop2 &lt;- read.csv(system.file("extdata", "aggregate_data_example_2.csv",</pre>
+                      <pre class="language-r">      "perc" = list(4, 5, "percent"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">25</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">493</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   package = "maicplus", mustWork = TRUE</pre>
+                      <pre class="language-r">      "bca" = list(4, 5, "bca")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">494</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ))</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">495</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' target_pop3 &lt;- read.csv(system.file("extdata", "aggregate_data_example_3.csv",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">28</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">496</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   package = "maicplus", mustWork = TRUE</pre>
+                      <pre class="language-r">    transform_estimate &lt;- switch(eff_measure,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">29</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">497</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ))</pre>
+                      <pre class="language-r">      "RD" = function(x) x * 100,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">30</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">498</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      "RR" = exp,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">31</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">499</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' target_pop &lt;- process_agd(target_pop)</pre>
+                      <pre class="language-r">      "OR" = exp</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">500</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' target_pop2 &lt;- process_agd(target_pop2)</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">33</td>
+                    <td class="num">501</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' target_pop3 &lt;- process_agd(target_pop3)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">34</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">502</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    res$inferential[["boot_est"]] &lt;- boot_res</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">35</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">503</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return pre-processed aggregate level data</pre>
+                      <pre class="language-r">    boot_res_AB &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">36</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">504</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      est = transform_estimate(boot_res$t0[1]),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">37</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">505</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      se = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">38</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">506</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">process_agd &lt;- function(raw_agd) {</pre>
+                      <pre class="language-r">      ci_l = transform_estimate(boot_ci[[l_u_index[[3]]]][l_u_index[[1]]]),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">39</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">507</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  raw_agd &lt;- as.data.frame(raw_agd)</pre>
+                      <pre class="language-r">      ci_u = transform_estimate(boot_ci[[l_u_index[[3]]]][l_u_index[[2]]]),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">40</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">508</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # make all column names to be capital letters to avoid different style</pre>
+                      <pre class="language-r">      pval = NA</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">41</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">509</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(raw_agd) &lt;- toupper(names(raw_agd))</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">42</td>
+                    <td class="num">510</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">43</td>
+                    <td class="num">511</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # define column name patterns[-]</pre>
+                      <pre class="language-r">    # boot results for A v C</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">44</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">512</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  must_exist &lt;- c("STUDY", "ARM", "N")</pre>
+                      <pre class="language-r">    boot_ci_ac &lt;- boot.ci(boot_res, type = boot_ci_type, w_obj = weights_object, index = c(4, 6))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">45</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">513</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  legal_suffix &lt;- c("MEAN", "MEDIAN", "SD", "COUNT", "PROP")</pre>
+                      <pre class="language-r">    boot_res_AC &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">46</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">514</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      est = transform_estimate(boot_res$t0[4]),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">47</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">515</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # swap "TREATMENT" column to "ARM", if applicable</pre>
+                      <pre class="language-r">      se = NA,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">48</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">516</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if ("TREATMENT" %in% names(raw_agd) &amp;&amp; (!"ARM" %in% names(raw_agd))) {</pre>
+                      <pre class="language-r">      ci_l = transform_estimate(boot_ci_ac[[l_u_index[[3]]]][l_u_index[[1]]]),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">49</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">517</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    raw_agd$ARM &lt;- raw_agd$TREATMENT</pre>
+                      <pre class="language-r">      ci_u = transform_estimate(boot_ci_ac[[l_u_index[[3]]]][l_u_index[[2]]]),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">50</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">518</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    raw_agd &lt;- raw_agd[, names(raw_agd) != "TREATMENT"]</pre>
+                      <pre class="language-r">      pval = NA</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">519</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">520</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">51</td>
+                    <td class="num">521</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    warning("'TREATMENT' column is renamed as 'ARM'")</pre>
+                      <pre class="language-r">    res$inferential[["boot_est"]] &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">52</td>
+                    <td class="num">522</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">53</td>
+                    <td class="num">523</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">54</td>
+                    <td class="num">524</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # check: must exist</pre>
+                      <pre class="language-r">  # : make analysis report table</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">55</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">525</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!all(must_exist %in% names(raw_agd))) {</pre>
+                      <pre class="language-r">  tags &lt;- paste0(c("IPD/", "weighted IPD/", "AgD/"), endpoint_name)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">56</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">526</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("At least 1 of the must-exists columns (STUDY, ARM, N) cannot be found in raw_agd!")</pre>
+                      <pre class="language-r">  res$inferential[["report_overall_robustCI"]] &lt;- rbind(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">57</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">527</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    report_table_binary(binobj_ipd, tag = tags[1], eff_measure = eff_measure),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">58</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">528</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    report_table_binary(binobj_ipd_adj, res_AC, tag = tags[2], eff_measure = eff_measure),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">59</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">529</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # check: legal suffix</pre>
+                      <pre class="language-r">    report_table_binary(binobj_agd, tag = tags[3], eff_measure = eff_measure),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">60</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">530</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  other_colnames &lt;- setdiff(names(raw_agd), must_exist)</pre>
+                      <pre class="language-r">    c(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">61</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">531</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ind1 &lt;- grepl("_", other_colnames, fixed = TRUE)</pre>
+                      <pre class="language-r">      paste0("** adj.", trt_ipd, " vs ", trt_agd),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">62</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">532</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ind2 &lt;- sapply(other_colnames, function(xx) {</pre>
+                      <pre class="language-r">      rep("--", 3),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">63</td>
-                    <td class="coverage">21<em>x</em></td>
+                    <td class="num">533</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    tmp &lt;- unlist(strsplit(xx, split = "_"))</pre>
+                      <pre class="language-r">      reformat(res_AB, pval_digits = 3)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">64</td>
-                    <td class="coverage">21<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">534</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    tmp[length(tmp)] # this deployment is robust to the cases that there are multiple _ in the column name</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">65</td>
+                    <td class="num">535</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">536</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">66</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">537</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ind2 &lt;- (ind2 %in% legal_suffix)</pre>
+                      <pre class="language-r">  if (is.null(res$inferential[["boot_est"]])) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">538</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    res$inferential[["report_overall_bootCI"]] &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">67</td>
+                    <td class="num">539</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">68</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">540</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_cols &lt;- other_colnames[ind1 &amp; ind2]</pre>
+                      <pre class="language-r">    res$inferential[["report_overall_bootCI"]] &lt;- rbind(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">69</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">541</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_agd &lt;- raw_agd[, c(must_exist, use_cols), drop = FALSE]</pre>
+                      <pre class="language-r">      report_table_binary(binobj_ipd, tag = tags[1], eff_measure = eff_measure),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">70</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">542</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!all(other_colnames %in% use_cols)) {</pre>
+                      <pre class="language-r">      report_table_binary(binobj_ipd_adj, boot_res_AC, tag = tags[2], eff_measure = eff_measure),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">71</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">543</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    warning(paste0(</pre>
+                      <pre class="language-r">      report_table_binary(binobj_agd, tag = tags[3], eff_measure = eff_measure),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">72</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">544</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "following columns are ignored since it does not follow the naming conventions:",</pre>
+                      <pre class="language-r">      c(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">73</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">545</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      paste(setdiff(other_colnames, use_cols), collapse = ",")</pre>
+                      <pre class="language-r">        paste0("** adj.", trt_ipd, " vs ", trt_agd),</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">546</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        rep("--", 3),</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">547</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        reformat(boot_res_AB, pval_digits = 3)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">74</td>
+                    <td class="num">548</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ))</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">75</td>
+                    <td class="num">549</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">76</td>
+                    <td class="num">550</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">77</td>
+                    <td class="num">551</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # If the aggregate data is divided by different arms, calculate pooled arm statistics using</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">78</td>
+                    <td class="num">552</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # complete_agd function; complete statistics is specified by ARM=="Total"</pre>
+                      <pre class="language-r">  # output</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">79</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">553</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!"total" %in% tolower(use_agd$ARM)) {</pre>
+                      <pre class="language-r">  res</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">80</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">554</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_agd &lt;- complete_agd(use_agd)</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/matching.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
                   <tr class="never">
-                    <td class="num">81</td>
+                    <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r"># Functions for matching step: estimation of individual weights</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">82</td>
+                    <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">83</td>
+                    <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # calculate percentage columns</pre>
+                      <pre class="language-r"># functions to be exported ---------------------------------------</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">84</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">4</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ind &lt;- grepl("_COUNT$", names(use_agd))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">85</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">5</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (any(ind)) {</pre>
+                      <pre class="language-r">#' Derive individual weights in the matching step of MAIC</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">86</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">6</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    for (i in which(ind)) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">87</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">7</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tmp_prop &lt;- use_agd[[i]] / use_agd$N</pre>
+                      <pre class="language-r">#' Assuming data is properly processed, this function takes individual patient data (IPD) with centered covariates</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">88</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # in case some count are not specified, but proportion are specified, copy over those proportions</pre>
+                      <pre class="language-r">#' (effect modifiers and/or prognostic variables) as input, and generates weights for each individual in IPD trial to</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">89</td>
+                    <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # this also means, in case count is specified, proportion is ignored even it is specified</pre>
+                      <pre class="language-r">#' match the covariates in aggregate data.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">90</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">10</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      prop_name_i &lt;- gsub("_COUNT$", "_PROP", names(use_agd)[i])</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">91</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">11</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (prop_name_i %in% names(use_agd)) {</pre>
+                      <pre class="language-r">#' @param data a numeric matrix, centered covariates of IPD, no missing value in any cell is allowed</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">92</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">        tmp_prop[is.na(tmp_prop)] &lt;- use_agd[is.na(tmp_prop), prop_name_i]</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">93</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">12</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        names(use_agd)[names(use_agd) == prop_name_i] &lt;- paste0(prop_name_i, "_redundant")</pre>
+                      <pre class="language-r">#' @param centered_colnames a character or numeric vector (column indicators) of centered covariates</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">94</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#' @param start_val a scalar, the starting value for all coefficients of the propensity score regression</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">95</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">14</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      use_agd[[i]] &lt;- tmp_prop</pre>
+                      <pre class="language-r">#' @param method a string, name of the optimization algorithm (see 'method' argument of \code{base::optim()}) The</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">96</td>
+                    <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">#'   default is `"BFGS"`, other options are `"Nelder-Mead"`, `"CG"`, `"L-BFGS-B"`, `"SANN"`, and `"Brent"`</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">97</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">16</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    names(use_agd) &lt;- gsub("_COUNT$", "_PROP", names(use_agd))</pre>
+                      <pre class="language-r">#' @param n_boot_iteration an integer, number of bootstrap iterations. By default is NULL which means bootstrapping</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">98</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#'   procedure will not be triggered, and hence the element `"boot"` of output list object will be NULL.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">99</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">18</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_agd &lt;- use_agd[, !grepl("_redundant$", names(use_agd))]</pre>
+                      <pre class="language-r">#' @param set_seed_boot a scalar, the random seed for conducting the bootstrapping, only relevant if</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">100</td>
+                    <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   \code{n_boot_iteration} is not NULL. By default, use seed 1234</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">101</td>
+                    <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # output</pre>
+                      <pre class="language-r">#' @param ... Additional `control` parameters passed to [stats::optim].</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">102</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">21</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  with(use_agd, use_agd[tolower(ARM) == "total", , drop = FALSE])</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">103</td>
+                    <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#' @return a list with the following 4 elements,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">104</td>
+                    <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' \describe{</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">105</td>
+                    <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   \item{data}{a data.frame, includes the input \code{data} with appended column 'weights' and 'scaled_weights'.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">106</td>
+                    <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Create dummy variables from categorical variables in an individual patient data (ipd)</pre>
+                      <pre class="language-r">#'   Scaled weights has a summation to be the number of rows in \code{data} that has no missing value in any of the</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">107</td>
+                    <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   effect modifiers}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">108</td>
+                    <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This is a convenient function to convert categorical variables into dummy binary variables.</pre>
+                      <pre class="language-r">#'   \item{centered_colnames}{column names of centered effect modifiers in \code{data}}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">109</td>
+                    <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This would be especially useful if the variable has more than two factors.</pre>
+                      <pre class="language-r">#'   \item{nr_missing}{number of rows in \code{data} that has at least 1 missing value in specified centered effect</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">110</td>
+                    <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Note that the original variable is kept after a variable is dummized.</pre>
+                      <pre class="language-r">#'   modifiers}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">111</td>
+                    <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   \item{ess}{effective sample size, square of sum divided by sum of squares}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">112</td>
+                    <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param raw_ipd ipd data that contains variable to dummize</pre>
+                      <pre class="language-r">#'   \item{opt}{R object returned by \code{base::optim()}, for assess convergence and other details}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">113</td>
+                    <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param dummize_cols vector of column names to binarize</pre>
+                      <pre class="language-r">#'   \item{boot}{a n by 2 by k array or NA, where n equals to number of rows in \code{data}, and k equals</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">114</td>
+                    <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param dummize_ref_level vector of reference level of the variables to binarize</pre>
+                      <pre class="language-r">#'      \code{n_boot_iteration}. The 2 columns in the second dimension include a column of numeric indexes of the rows</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">115</td>
+                    <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'      in \code{data} that are selected at a bootstrapping iteration and a column of weights. \code{boot} is NA when</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">116</td>
+                    <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">#'      argument \code{n_boot_iteration} is set as NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">117</td>
+                    <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data(adsl_twt)</pre>
+                      <pre class="language-r">#'   }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">118</td>
+                    <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' dummize_ipd(adsl_twt, dummize_cols = c("SEX"), dummize_ref_level = c("Male"))</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">119</td>
+                    <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">120</td>
+                    <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return ipd with dummized columns</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">121</td>
+                    <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' data(agd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">122</td>
+                    <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' data(adsl_sat)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">123</td>
+                    <td class="num">42</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">dummize_ipd &lt;- function(raw_ipd, dummize_cols, dummize_ref_level) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">124</td>
-                    <td class="coverage">3<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  for (i in seq_along(dummize_cols)) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">125</td>
-                    <td class="coverage">3<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    yy &lt;- raw_ipd[[dummize_cols[i]]]</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">126</td>
-                    <td class="coverage">3<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    yy_levels &lt;- na.omit(unique(yy))</pre>
+                      <pre class="language-r">#' ipd_centered &lt;- center_ipd(ipd = adsl_sat, agd = process_agd(agd))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">127</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">43</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    yy &lt;- factor(as.character(yy), levels = c(dummize_ref_level[i], setdiff(yy_levels, dummize_ref_level[i])))</pre>
+                      <pre class="language-r">#' centered_colnames &lt;- grep("_CENTERED", colnames(ipd_centered), value = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">128</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">44</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    new_yy &lt;- sapply(levels(yy)[-1], function(j) {</pre>
+                      <pre class="language-r">#' centered_colnames</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">129</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">45</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      as.numeric(yy == j)</pre>
+                      <pre class="language-r">#' weighted_data &lt;- estimate_weights(data = ipd_centered, centered_colnames = centered_colnames)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">130</td>
+                    <td class="num">46</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' \donttest{</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">131</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">47</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    new_yy &lt;- as.data.frame(new_yy)</pre>
+                      <pre class="language-r">#' # To later estimate bootstrap confidence intervals, we calculate the weights</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">132</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">48</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    names(new_yy) &lt;- toupper(paste(dummize_cols[i], levels(yy)[-1], sep = "_"))</pre>
+                      <pre class="language-r">#' # for the bootstrap samples:</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">133</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">49</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    raw_ipd &lt;- cbind(raw_ipd, new_yy)</pre>
+                      <pre class="language-r">#' weighted_data_boot &lt;- estimate_weights(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">134</td>
+                    <td class="num">50</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#'   data = ipd_centered, centered_colnames = centered_colnames, n_boot_iteration = 500</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">135</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">51</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  raw_ipd</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">136</td>
+                    <td class="num">52</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">137</td>
+                    <td class="num">53</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">138</td>
+                    <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">139</td>
+                    <td class="num">55</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Center individual patient data (IPD) variables using aggregate data averages</pre>
+                      <pre class="language-r">estimate_weights &lt;- function(data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">140</td>
+                    <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                             centered_colnames = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">141</td>
+                    <td class="num">57</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This function subtracts IPD variables (prognostic variables and/or effect modifiers)</pre>
+                      <pre class="language-r">                             start_val = 0,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">142</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' by the aggregate data averages. This centering is needed in order to calculate weights.</pre>
+                      <pre class="language-r">                             method = "BFGS",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">143</td>
+                    <td class="num">59</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' IPD and aggregate data variable names should match.</pre>
+                      <pre class="language-r">                             n_boot_iteration = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">144</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                             set_seed_boot = 1234,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">145</td>
+                    <td class="num">61</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ipd IPD variable names should match the aggregate data names without the suffix.</pre>
+                      <pre class="language-r">                             ...) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">146</td>
+                    <td class="num">62</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This would involve either changing the aggregate data name or the ipd name.</pre>
+                      <pre class="language-r">  # pre check</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">147</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">63</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' For instance, if we binarize SEX variable with MALE as a reference using [dummize_ipd],</pre>
+                      <pre class="language-r">  ch1 &lt;- is.data.frame(data)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">148</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">64</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' function names the new variable as SEX_MALE.</pre>
+                      <pre class="language-r">  if (!ch1) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">149</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">65</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' In this case, SEX_MALE should also be available in the aggregate data.</pre>
+                      <pre class="language-r">    stop("'data' is not a data.frame")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">150</td>
+                    <td class="num">66</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param agd pre-processed aggregate data which contain STUDY, ARM, and N. Variable names</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">151</td>
+                    <td class="num">67</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' should be followed by legal suffixes (i.e. MEAN, MEDIAN, SD, or PROP). Note that COUNT</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">152</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">68</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' suffix is no longer accepted.</pre>
+                      <pre class="language-r">  ch2 &lt;- (!is.null(centered_colnames))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">153</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">69</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">  if (ch2 &amp;&amp; is.numeric(centered_colnames)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">154</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">70</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # load in IPD</pre>
+                      <pre class="language-r">    ch2b &lt;- any(centered_colnames &lt; 1 | centered_colnames &gt; ncol(data))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">155</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">71</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data(adsl_sat)</pre>
+                      <pre class="language-r">    if (ch2b) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">156</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">72</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' adsl &lt;- dummize_ipd(adsl_sat, dummize_cols = c("SEX"), dummize_ref_level = c("Female"))</pre>
+                      <pre class="language-r">      stop("specified centered_colnames are out of bound")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">157</td>
+                    <td class="num">73</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">158</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">74</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Reading aggregate data by Excel</pre>
+                      <pre class="language-r">  } else if (ch2 &amp;&amp; is.character(centered_colnames)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">159</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">75</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' target_pop &lt;- read.csv(</pre>
+                      <pre class="language-r">    ch2b &lt;- !all(centered_colnames %in% names(data))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">160</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">76</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   system.file("extdata", "aggregate_data_example_1.csv", package = "maicplus", mustWork = TRUE)</pre>
+                      <pre class="language-r">    if (ch2b) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">161</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">77</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">      stop("1 or more specified centered_colnames are not found in 'data'")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">162</td>
+                    <td class="num">78</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' agd &lt;- process_agd(target_pop)</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">163</td>
+                    <td class="num">79</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">164</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">80</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Alternatively, you can specify aggregate data manually in data frame</pre>
+                      <pre class="language-r">    stop("'centered_colnames' should be either a numeric or character vector")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">165</td>
+                    <td class="num">81</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data(agd)</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">166</td>
+                    <td class="num">82</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ipd_centered &lt;- center_ipd(ipd = adsl, agd = agd)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">167</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">83</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  ch3 &lt;- sapply(centered_colnames, function(ii) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">168</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">84</td>
+                    <td class="coverage">66<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return centered ipd using aggregate level data averages</pre>
+                      <pre class="language-r">    !is.numeric(data[[ii]])</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">169</td>
+                    <td class="num">85</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">170</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">86</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  if (any(ch3)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">171</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">87</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">center_ipd &lt;- function(ipd, agd) {</pre>
+                      <pre class="language-r">    stop(paste0(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">172</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">88</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # regularized column name patterns</pre>
+                      <pre class="language-r">      "following columns of 'data' are not numeric for the calculation:",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">173</td>
-                    <td class="coverage">8<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">89</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  must_exist &lt;- c("STUDY", "ARM", "N")</pre>
+                      <pre class="language-r">      paste(which(ch3), collapse = ",")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">174</td>
-                    <td class="coverage">8<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">90</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  legal_suffix &lt;- c("MEAN", "MEDIAN", "SD", "PROP")</pre>
+                      <pre class="language-r">    ))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">175</td>
-                    <td class="coverage">8<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">91</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  suffix_pat &lt;- paste(paste0("_", legal_suffix, "$"), collapse = "|")</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">176</td>
+                    <td class="num">92</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">177</td>
-                    <td class="coverage">8<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">93</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  for (i in seq_len(nrow(agd))) { # study i</pre>
+                      <pre class="language-r">  # prepare data for optimization</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">178</td>
-                    <td class="coverage">8<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">94</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    study_id &lt;- agd$STUDY[i]</pre>
+                      <pre class="language-r">  if (is.null(centered_colnames)) centered_colnames &lt;- seq_len(ncol(data))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">179</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="num">95</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_agd &lt;- agd[i, !names(agd) %in% must_exist, drop = FALSE]</pre>
+                      <pre class="language-r">  EM &lt;- data[, centered_colnames, drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">180</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="num">96</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    param_id &lt;- gsub(suffix_pat, "", names(use_agd))</pre>
+                      <pre class="language-r">  ind &lt;- apply(EM, 1, function(xx) any(is.na(xx)))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">181</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">97</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  nr_missing &lt;- sum(ind)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">182</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="num">98</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    for (j in seq_len(ncol(use_agd))) { # effect modifier j</pre>
+                      <pre class="language-r">  rows_with_missing &lt;- which(ind)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">183</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">99</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (is.na(use_agd[[j]])) next</pre>
+                      <pre class="language-r">  EM &lt;- as.matrix(EM[!ind, , drop = FALSE])</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">184</td>
+                    <td class="num">100</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">185</td>
-                    <td class="coverage">56<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      ipd_param &lt;- param_id[j]</pre>
-                    </td>
-                  </tr>
                   <tr class="never">
-                    <td class="num">186</td>
+                    <td class="num">101</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # estimate weights</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">187</td>
-                    <td class="coverage">56<em>x</em></td>
+                    <td class="num">102</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (grepl("_MEAN$|_PROP$", names(use_agd)[j])) {</pre>
+                      <pre class="language-r">  opt1 &lt;- optimise_weights(matrix = EM, par = rep(start_val, ncol(EM)), method = method, ...)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">188</td>
-                    <td class="coverage">32<em>x</em></td>
+                    <td class="num">103</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ipd[[paste0(ipd_param, "_", "CENTERED")]] &lt;- ipd[[ipd_param]] - use_agd[[j]]</pre>
+                      <pre class="language-r">  alpha &lt;- opt1$alpha</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">189</td>
-                    <td class="coverage">24<em>x</em></td>
+                    <td class="num">104</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else if (grepl("_MEDIAN$", names(use_agd)[j])) {</pre>
+                      <pre class="language-r">  wt &lt;- opt1$wt</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">190</td>
-                    <td class="coverage">16<em>x</em></td>
+                    <td class="num">105</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ipd[[paste0(ipd_param, "_MEDIAN_", "CENTERED")]] &lt;- ipd[[ipd_param]] &gt; use_agd[[j]]</pre>
+                      <pre class="language-r">  wt_rs &lt;- (wt / sum(wt)) * nrow(EM)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">191</td>
-                    <td class="coverage">16<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">106</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ipd[[paste0(ipd_param, "_MEDIAN_", "CENTERED")]] &lt;- ipd[[paste0(ipd_param, "_MEDIAN_", "CENTERED")]] - 0.5</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">192</td>
-                    <td class="coverage">8<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">107</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else if (grepl("_SD$", names(use_agd)[j])) {</pre>
+                      <pre class="language-r">  # bootstrapping</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">193</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="num">108</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ipd[[paste0(ipd_param, "_SQUARED_", "CENTERED")]] &lt;- ipd[[ipd_param]]^2</pre>
+                      <pre class="language-r">  outboot &lt;- if (is.null(n_boot_iteration)) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">194</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="num">109</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        tmp_aim &lt;- use_agd[[j]]^2 + (use_agd[[paste0(ipd_param, "_MEAN")]]^2)</pre>
+                      <pre class="language-r">    boot_seed &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">195</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="num">110</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ipd[[paste0(ipd_param, "_SQUARED_", "CENTERED")]] &lt;- ipd[[paste0(ipd_param, "_SQUARED_", "CENTERED")]] - tmp_aim</pre>
+                      <pre class="language-r">    boot_strata &lt;- NULL</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">196</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">111</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">    NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">197</td>
+                    <td class="num">112</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    } # end of j</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">198</td>
+                    <td class="num">113</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } # end of i</pre>
+                      <pre class="language-r">    # Make sure to leave '.Random.seed' as-is on exit</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">199</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">114</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    old_seed &lt;- globalenv()$.Random.seed</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">200</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">115</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # output</pre>
+                      <pre class="language-r">    on.exit(suspendInterrupts(set_random_seed(old_seed)))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">201</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="num">116</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ipd</pre>
+                      <pre class="language-r">    set.seed(set_seed_boot)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">202</td>
+                    <td class="num">117</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">203</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">118</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    rowid_in_data &lt;- which(!ind)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">204</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">119</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    arms &lt;- factor(data$ARM[rowid_in_data])</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">205</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">120</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Calculate pooled arm statistics in Aggregated Data (AgD) based on arm-specific statistics</pre>
+                      <pre class="language-r">    boot_statistic &lt;- function(d, w) optimise_weights(d[w, ], par = alpha, method = method, ...)$wt[, 1]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">206</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">121</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    boot_out &lt;- boot(EM, statistic = boot_statistic, R = n_boot_iteration, strata = arms)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">207</td>
+                    <td class="num">122</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This is a convenient function to pool arm statistics. This function is called</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">208</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">123</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' within process_agd and when the ARM is not equal to "Total". Note pooled</pre>
+                      <pre class="language-r">    boot_array &lt;- array(dim = list(nrow(EM), 2, n_boot_iteration))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">209</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">124</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' median can't be calculated and it is only an approximation.</pre>
+                      <pre class="language-r">    dimnames(boot_array) &lt;- list(sampled_patient = NULL, c("rowid", "weight"), bootstrap_iteration = NULL)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">210</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">125</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    boot_array[, 1, ] &lt;- t(boot.array(boot_out, TRUE))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">211</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">126</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param use_agd aggregated data that is processed within process_agd</pre>
+                      <pre class="language-r">    boot_array[, 2, ] &lt;- t(boot_out$t)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">212</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">127</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    boot_seed &lt;- boot_out$seed</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">213</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">128</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Complete N, count, mean, sd, and median for the pooled arm</pre>
+                      <pre class="language-r">    boot_strata &lt;- boot_out$strata</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">214</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">129</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    boot_array</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">215</td>
+                    <td class="num">130</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">complete_agd &lt;- function(use_agd) {</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">216</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">131</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_agd &lt;- as.data.frame(use_agd)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">217</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">132</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_agd &lt;- with(use_agd, {</pre>
+                      <pre class="language-r">  # append weights to data</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">218</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">133</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_agd[tolower(ARM) != "total", , drop = FALSE]</pre>
+                      <pre class="language-r">  data$weights &lt;- NA</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">219</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">134</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">  data$weights[!ind] &lt;- wt</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">220</td>
+                    <td class="num">135</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">221</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (nrow(use_agd) &lt; 2) stop("error in call complete_agd: need to have at least 2 rows that ARM!='total' ")</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">222</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">223</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">136</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  rowId &lt;- nrow(use_agd) + 1</pre>
+                      <pre class="language-r">  data$scaled_weights &lt;- NA</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">224</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">137</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_agd[rowId, ] &lt;- NA</pre>
+                      <pre class="language-r">  data$scaled_weights[!ind] &lt;- wt_rs</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">225</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">138</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_agd$STUDY[rowId] &lt;- use_agd$STUDY[1]</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">226</td>
+                    <td class="num">139</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_agd$ARM[rowId] &lt;- "total"</pre>
+                      <pre class="language-r">  if (is.numeric(centered_colnames)) centered_colnames &lt;- names(data)[centered_colnames]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">227</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">228</td>
+                    <td class="num">141</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # complete N and count</pre>
+                      <pre class="language-r">  # Output</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">229</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">142</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  NN &lt;- use_agd[["N"]][rowId] &lt;- sum(use_agd[["N"]], na.rm = TRUE)</pre>
+                      <pre class="language-r">  outdata &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">230</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">143</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  nn &lt;- use_agd[["N"]][-rowId]</pre>
+                      <pre class="language-r">    data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">231</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">144</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  for (i in grep("_COUNT$", names(use_agd), value = TRUE)) {</pre>
+                      <pre class="language-r">    centered_colnames = centered_colnames,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">232</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">145</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_agd[[i]][rowId] &lt;- sum(use_agd[[i]][-rowId], na.rm = TRUE)</pre>
+                      <pre class="language-r">    nr_missing = nr_missing,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">233</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">146</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    ess = sum(wt)^2 / sum(wt^2),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">234</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">147</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    opt = opt1$opt,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">235</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">148</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # complete MEAN</pre>
+                      <pre class="language-r">    boot = outboot,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">236</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">149</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  for (i in grep("_MEAN$", names(use_agd), value = TRUE)) {</pre>
+                      <pre class="language-r">    boot_seed = boot_seed,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">237</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">150</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_agd[[i]][rowId] &lt;- sum(use_agd[[i]][-rowId] * nn) / NN</pre>
+                      <pre class="language-r">    boot_strata = boot_strata,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">238</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">151</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    rows_with_missing = rows_with_missing</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">239</td>
+                    <td class="num">152</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">240</td>
+                    <td class="num">153</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # complete SD</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">241</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">154</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  for (i in grep("_SD$", names(use_agd), value = TRUE)) {</pre>
+                      <pre class="language-r">  class(outdata) &lt;- c("maicplus_estimate_weights", "list")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">242</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">155</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_agd[[i]][rowId] &lt;- sqrt(sum(use_agd[[i]][-rowId]^2 * (nn - 1)) / (NN - 1))</pre>
+                      <pre class="language-r">  outdata</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">243</td>
+                    <td class="num">156</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">244</td>
+                    <td class="num">157</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">245</td>
+                    <td class="num">158</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # complete MEDIAN, approximately!!</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">246</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  for (i in grep("_MEDIAN$", names(use_agd), value = TRUE)) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">247</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    use_agd[[i]][rowId] &lt;- mean(use_agd[[i]][-rowId])</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">248</td>
+                    <td class="num">159</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' Estimate weights using `optim`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">249</td>
+                    <td class="num">160</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">250</td>
+                    <td class="num">161</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # output</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">251</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  use_agd</pre>
+                      <pre class="language-r">#' @param matrix Matrix of data to be used for estimating weights</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">252</td>
+                    <td class="num">162</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#' @param par Vector of starting values for the parameters with length equal to the number of columns in `matrix`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">253</td>
+                    <td class="num">163</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param method Method parameter passed to [stats::optim]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">254</td>
+                    <td class="num">164</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param ... Additional `control` parameters passed to [stats::optim]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">255</td>
+                    <td class="num">165</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' helper function: transform TTE ADaM data to suitable input for survival R package</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">256</td>
+                    <td class="num">166</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @return List containing estimated `alpha` values and `wt` weights for all rows of matrix</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">257</td>
+                    <td class="num">167</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param dd data frame, ADTTE read via `haven::read_sas`</pre>
+                      <pre class="language-r">#' @noRd</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">258</td>
+                    <td class="num">168</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param time_scale a character string, 'years', 'months', 'weeks' or 'days', time unit of median survival time</pre>
+                      <pre class="language-r">optimise_weights &lt;- function(matrix,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">259</td>
+                    <td class="num">169</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt values to include in treatment column</pre>
+                      <pre class="language-r">                             par = rep(0, ncol(matrix)),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">260</td>
+                    <td class="num">170</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                             method = "BFGS",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">261</td>
+                    <td class="num">171</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a data frame that can be used as input to `survival::Surv`</pre>
+                      <pre class="language-r">                             maxit = 300,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">262</td>
+                    <td class="num">172</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                             trace = 0,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">263</td>
+                    <td class="num">173</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ext_tte_transfer &lt;- function(dd, time_scale = "months", trt = NULL) {</pre>
+                      <pre class="language-r">                             ...) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">264</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">174</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  time_scale &lt;- match.arg(time_scale, choices = c("years", "months", "weeks", "days"))</pre>
+                      <pre class="language-r">  if (!all(is.numeric(par) || is.finite(par), length(par) == ncol(matrix))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">265</td>
+                    <td class="num">175</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  time_units &lt;- get_time_conversion(time_scale)</pre>
+                      <pre class="language-r">    stop("par must be a numeric vector with finite values of length equal to the number of columns in 'matrix'")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">266</td>
+                    <td class="num">176</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">267</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">177</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if ("CENSOR" %in% names(dd)) {</pre>
+                      <pre class="language-r">  opt1 &lt;- optim(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">268</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">178</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    dd &lt;- dd[!is.na(dd$CENSOR), ]</pre>
+                      <pre class="language-r">    par = par,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">269</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">179</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    dd$status &lt;- as.numeric(dd$CENSOR == 0)</pre>
+                      <pre class="language-r">    fn = function(alpha, X) sum(exp(X %*% alpha)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">270</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">180</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    gr = function(alpha, X) colSums(sweep(X, 1, exp(X %*% alpha), "*")),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">271</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">181</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if ("EVENT" %in% names(dd)) {</pre>
+                      <pre class="language-r">    X = matrix,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">272</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">182</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    dd$status &lt;- as.numeric(as.character(dd$EVENT))</pre>
+                      <pre class="language-r">    method = method,</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">183</td>
+                    <td class="coverage">544<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    control = list(maxit = maxit, trace = trace, ...)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">273</td>
+                    <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">274</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">185</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if ("TIME" %in% names(dd)) {</pre>
+                      <pre class="language-r">  if (opt1$convergence != 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">275</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">186</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    dd$AVAL &lt;- as.numeric(as.character(dd$TIME))</pre>
+                      <pre class="language-r">    warning(</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">187</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      "optim() did not converge. ",</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">188</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      opt1$message,</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">189</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      "\nSee ?optim for more information on convergence code: ", opt1$convergence</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">276</td>
+                    <td class="num">190</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">277</td>
+                    <td class="num">191</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">278</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">192</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  dd$time &lt;- dd$AVAL * time_units</pre>
+                      <pre class="language-r">  list(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">279</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">193</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!is.null(trt)) dd$treatment &lt;- trt</pre>
+                      <pre class="language-r">    opt = opt1,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">280</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">194</td>
+                    <td class="coverage">544<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  as.data.frame(dd)</pre>
+                      <pre class="language-r">    alpha = opt1$par,</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">195</td>
+                    <td class="coverage">544<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    wt = exp(matrix %*% opt1$par)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">281</td>
+                    <td class="num">196</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">197</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/reporting.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">198</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' helper function: sort out a nice report table to summarize survival analysis results</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">2</td>
+                    <td class="num">199</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' Calculate Statistics for Weight Plot Legend</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">200</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">201</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param coxobj returned object from \code{\link[survival]{coxph}}</pre>
+                      <pre class="language-r">#' Calculates ESS reduction and median weights which is used to create legend for weights plot</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">202</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param medSurvobj returned object from \code{\link{medSurv_makeup}}</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">5</td>
+                    <td class="num">203</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param tag a string, by default NULL, if specified, an extra 1st column is created in the output</pre>
+                      <pre class="language-r">#' @param weighted_data object returned after calculating weights using [estimate_weights]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">6</td>
+                    <td class="num">204</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">7</td>
+                    <td class="num">205</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a data frame with sample size, incidence rate, median survival time with 95% CI, hazard ratio estimate with</pre>
+                      <pre class="language-r">#' @return list of ESS, ESS reduction, median value of scaled and unscaled weights, and missing count</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">206</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' 95% CI and Wald test of hazard ratio</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">9</td>
+                    <td class="num">207</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' data("weighted_sat")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">10</td>
+                    <td class="num">208</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' calculate_weights_legend(weighted_sat)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">11</td>
+                    <td class="num">209</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">12</td>
+                    <td class="num">210</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">report_table_tte &lt;- function(coxobj, medSurvobj, tag = NULL) {</pre>
+                      <pre class="language-r">#' @keywords internal</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">13</td>
+                    <td class="num">211</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # descriptive part</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">14</td>
-                    <td class="coverage">15<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">212</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  N &lt;- medSurvobj$n.max</pre>
+                      <pre class="language-r">calculate_weights_legend &lt;- function(weighted_data) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">15</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">213</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  N.EVNT &lt;- medSurvobj$events</pre>
+                      <pre class="language-r">  if (!inherits(weighted_data, "maicplus_estimate_weights")) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">16</td>
-                    <td class="coverage">15<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">214</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  N.EVNT.PERC &lt;- round(N.EVNT * 100 / N, 1)</pre>
+                      <pre class="language-r">    stop("weighted_data must be class `maicplus_estimate_weights` generated by estimate_weights()")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">17</td>
-                    <td class="coverage">15<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">215</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  N &lt;- round(N, 1) # not necessary integer</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">18</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">216</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  N.EVNT &lt;- round(N.EVNT, 1) # not necessary integer</pre>
+                      <pre class="language-r">  ess &lt;- weighted_data$ess</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">19</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">217</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  meds_report &lt;- format(round(medSurvobj[, c("median", "0.95LCL", "0.95UCL")], 1), nsmall = 1)</pre>
+                      <pre class="language-r">  wt &lt;- weighted_data$data$weights</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">20</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">218</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  meds_report &lt;- apply(meds_report, 1, function(xx) paste0(xx[1], "[", xx[2], ";", xx[3], "]"))</pre>
+                      <pre class="language-r">  wt_scaled &lt;- weighted_data$data$scaled_weights</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">21</td>
+                    <td class="num">219</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">22</td>
+                    <td class="num">220</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # inferential part</pre>
+                      <pre class="language-r">  # calculate sample size and exclude NA from wt</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">23</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">221</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  hr_res &lt;- format(round(summary(coxobj)$conf.int[-2], 2), nsmall = 2)</pre>
+                      <pre class="language-r">  nr_na &lt;- sum(is.na(wt))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">24</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">222</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  hr_res &lt;- paste0(hr_res[1], "[", hr_res[2], ";", hr_res[3], "]")</pre>
+                      <pre class="language-r">  n &lt;- length(wt) - nr_na</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">25</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">223</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  hr_pval &lt;- format(round(summary(coxobj)$waldtest[3], 3), nsmall = 3)</pre>
+                      <pre class="language-r">  wt &lt;- na.omit(wt)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">26</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">224</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (hr_pval == "0.000") hr_pval &lt;- "&lt;0.001"</pre>
+                      <pre class="language-r">  wt_scaled &lt;- na.omit(wt_scaled)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">225</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">28</td>
+                    <td class="num">226</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # assemble the table</pre>
+                      <pre class="language-r">  # calculate ess reduction and median weights</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">29</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">227</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  desc_res &lt;- cbind(</pre>
+                      <pre class="language-r">  ess_reduction &lt;- (1 - (ess / n)) * 100</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">30</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">228</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    medSurvobj[, "treatment", drop = FALSE],</pre>
+                      <pre class="language-r">  wt_median &lt;- median(wt)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">31</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">229</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    data.frame(</pre>
+                      <pre class="language-r">  wt_scaled_median &lt;- median(wt_scaled)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">32</td>
-                    <td class="coverage">15<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">230</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "N" = N,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">33</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">231</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "n.events(%)" = paste0(N.EVNT, "(", format(N.EVNT.PERC, nsmall = 1), ")"),</pre>
+                      <pre class="language-r">  list(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">34</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">232</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "median[95% CI]" = meds_report,</pre>
+                      <pre class="language-r">    ess = round(ess, 2),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">35</td>
-                    <td class="coverage">15<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      check.names = FALSE</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">36</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">37</td>
-                    <td class="coverage"></td>
+                    <td class="num">233</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">    ess_reduction = round(ess_reduction, 2),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">38</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">234</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  desc_res &lt;- cbind(desc_res[c(2, 1), ], "HR[95% CI]" = c(hr_res, ""), "p-Value" = c(hr_pval, ""))</pre>
+                      <pre class="language-r">    wt_median = round(wt_median, 4),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">39</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">235</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(desc_res)[3] &lt;- "n.events(%)" # cbind changes column name</pre>
+                      <pre class="language-r">    wt_scaled_median = round(wt_scaled_median, 4),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">40</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">236</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    nr_na = nr_na</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">41</td>
+                    <td class="num">237</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # add first tag column if applicable</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">42</td>
-                    <td class="coverage">15<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (!is.null(tag)) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">43</td>
-                    <td class="coverage">15<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    desc_res &lt;- cbind(data.frame(Matching = rep(tag, nrow(desc_res))), desc_res)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">44</td>
-                    <td class="coverage">15<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    desc_res$Matching[duplicated(desc_res$Matching)] &lt;- ""</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">45</td>
+                    <td class="num">238</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">46</td>
+                    <td class="num">239</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">47</td>
+                    <td class="num">240</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # output</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">48</td>
-                    <td class="coverage">15<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  desc_res</pre>
+                      <pre class="language-r">#' Plot MAIC weights in a histogram with key statistics in legend</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">49</td>
+                    <td class="num">241</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">50</td>
+                    <td class="num">242</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' Generates a base R histogram of weights. Default is to plot either unscaled or scaled weights and not both.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">51</td>
+                    <td class="num">243</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' helper function: sort out a nice report table to summarize binary analysis results</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">52</td>
+                    <td class="num">244</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @param weighted_data object returned after calculating weights using [estimate_weights]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">53</td>
+                    <td class="num">245</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param binobj object from glm()</pre>
+                      <pre class="language-r">#' @param bin_col a string, color for the bins of histogram</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">54</td>
+                    <td class="num">246</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param weighted_result object res_AB</pre>
+                      <pre class="language-r">#' @param vline_col a string, color for the vertical line in the histogram</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">55</td>
+                    <td class="num">247</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param eff_measure a string, binary effect measure, could be "OR", "RR", "RD"</pre>
+                      <pre class="language-r">#' @param main_title title of the plot</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">56</td>
+                    <td class="num">248</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param tag a string, by default NULL, if specified, an extra 1st column is created in the output</pre>
+                      <pre class="language-r">#' @param scaled_weights an indicator for using scaled weights instead of regular weights</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">57</td>
+                    <td class="num">249</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">58</td>
+                    <td class="num">250</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a data frame with sample size, incidence rate, estimate of binary effect measure with</pre>
+                      <pre class="language-r">#' @return a plot of unscaled or scaled weights</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">59</td>
+                    <td class="num">251</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' 95% CI and Wald test of hazard ratio</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">60</td>
+                    <td class="num">252</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">61</td>
+                    <td class="num">253</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">plot_weights_base &lt;- function(weighted_data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">62</td>
+                    <td class="num">254</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                              bin_col, vline_col, main_title,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">63</td>
+                    <td class="num">255</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">report_table_binary &lt;- function(binobj, weighted_result = NULL, eff_measure = c("OR", "RD", "RR"), tag = NULL) {</pre>
+                      <pre class="language-r">                              scaled_weights) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">64</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">256</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  weighted &lt;- ifelse(is.null(weighted_result), FALSE, TRUE)</pre>
+                      <pre class="language-r">  weights_stat &lt;- calculate_weights_legend(weighted_data)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">65</td>
+                    <td class="num">257</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # descriptive part</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">66</td>
-                    <td class="coverage">6<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  ARM &lt;- levels(binobj$data$ARM)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">67</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">258</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!weighted) {</pre>
+                      <pre class="language-r">  if (scaled_weights) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">68</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">259</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    N &lt;- tapply(binobj$data$USUBJID, binobj$data$ARM, length)</pre>
+                      <pre class="language-r">    wt &lt;- weighted_data$data$scaled_weights</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">69</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">260</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    N.EVNT &lt;- tapply(binobj$data$RESPONSE, binobj$data$ARM, sum)</pre>
+                      <pre class="language-r">    median_wt &lt;- weights_stat$wt_scaled_median</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">70</td>
+                    <td class="num">261</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">71</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">262</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    N &lt;- tapply(binobj$data$weights, binobj$data$ARM, length)</pre>
+                      <pre class="language-r">    wt &lt;- weighted_data$data$weights</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">72</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">263</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    N.EVNT &lt;- tapply(binobj$data$weights * binobj$data$RESPONSE, binobj$data$ARM, sum)</pre>
+                      <pre class="language-r">    median_wt &lt;- weights_stat$wt_median</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">73</td>
+                    <td class="num">264</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">74</td>
-                    <td class="coverage">6<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  N.EVNT.PERC &lt;- round(N.EVNT * 100 / N, 1)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">75</td>
-                    <td class="coverage">6<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  N.EVNT &lt;- round(N.EVNT, 1)</pre>
-                    </td>
-                  </tr>
                   <tr class="never">
-                    <td class="num">76</td>
+                    <td class="num">265</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">77</td>
+                    <td class="num">266</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # inferential part</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">78</td>
-                    <td class="coverage">6<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (!weighted) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">79</td>
-                    <td class="coverage">3<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    bin_res_est &lt;- coef(binobj)[2]</pre>
+                      <pre class="language-r">  # prepare legend</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">80</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">267</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bin_res_ci &lt;- confint(binobj, parm = 2, test = "LRT", trace = FALSE)</pre>
+                      <pre class="language-r">  plot_legend &lt;- c(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">81</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">268</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bin_res &lt;- c(bin_res_est, bin_res_ci)</pre>
+                      <pre class="language-r">    paste0("Median = ", median_wt),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">82</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">269</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (eff_measure != "RD") bin_res &lt;- exp(bin_res)</pre>
+                      <pre class="language-r">    paste0("ESS = ", weights_stat$ess),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">83</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">270</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bin_res &lt;- round(bin_res, 2) |&gt; format(nsmall = 2)</pre>
+                      <pre class="language-r">    paste0("Reduction% = ", weights_stat$ess_reduct)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">84</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">271</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bin_res &lt;- paste0(bin_res[1], "[", bin_res[2], ";", bin_res[3], "]")</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">85</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">272</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bin_pval &lt;- round(summary(binobj)$coefficients[2, 4], 3) |&gt; format(nsmall = 3)</pre>
+                      <pre class="language-r">  plot_lty &lt;- c(2, NA, NA)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">86</td>
+                    <td class="num">273</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">87</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">274</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bin_res &lt;- round(unlist(weighted_result[c("est", "ci_l", "ci_u")]), 2) |&gt; format(nsmall = 2)</pre>
+                      <pre class="language-r">  if (weights_stat$nr_na &gt; 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">88</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">275</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bin_res &lt;- paste0(bin_res[1], "[", bin_res[2], ";", bin_res[3], "]")</pre>
+                      <pre class="language-r">    plot_legend &lt;- c(plot_legend, paste0("#Missing Weights = ", weights_stat$nr_na))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">89</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">276</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bin_pval &lt;- round(weighted_result$pval, 3) |&gt; format(nsmall = 3)</pre>
+                      <pre class="language-r">    plot_lty &lt;- c(plot_lty, NA)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">90</td>
+                    <td class="num">277</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">91</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (bin_pval == "0.000") bin_pval &lt;- "&lt;0.001"</pre>
-                    </td>
-                  </tr>
                   <tr class="never">
-                    <td class="num">92</td>
+                    <td class="num">278</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">93</td>
+                    <td class="num">279</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # assemble the table</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">94</td>
-                    <td class="coverage">6<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  desc_res &lt;- data.frame(</pre>
+                      <pre class="language-r">  # plot</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">95</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">280</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    "treatment" = ARM,</pre>
+                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">96</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">281</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    "N" = N,</pre>
+                      <pre class="language-r">  par(mgp = c(2.3, 0.5, 0), cex.axis = 0.9, cex.lab = 0.95, bty = "n")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">97</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">282</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    "n.events(%)" = paste0(N.EVNT, "(", format(N.EVNT.PERC, nsmall = 1), ")")</pre>
+                      <pre class="language-r">  on.exit(par(original_par))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">98</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">283</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">  hist(wt, border = "white", col = bin_col, main = main_title, breaks = 20, yaxt = "n", xlab = "")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">99</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">284</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  axis(2, las = 1)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">100</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">285</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  desc_res &lt;- cbind(desc_res[c(2, 1), ], "xx[95% CI]" = c(bin_res, ""), "p-Value" = c(bin_pval, ""))</pre>
+                      <pre class="language-r">  abline(v = median(wt), lty = 2, col = vline_col, lwd = 2)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">101</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">286</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(desc_res)[ncol(desc_res) - 1] &lt;- paste0(eff_measure, "[95% CI]")</pre>
+                      <pre class="language-r">  legend("topright", bty = "n", lty = plot_lty, cex = 0.8, legend = plot_legend)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">102</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">287</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(desc_res)[3] &lt;- "n.events(%)" # cbind changes column name</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">103</td>
+                    <td class="num">288</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">104</td>
+                    <td class="num">289</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # add first tag column if applicable</pre>
+                      <pre class="language-r">#' Plot MAIC weights in a histogram with key statistics in legend using `ggplot2`</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">105</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">290</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!is.null(tag)) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">106</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">291</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    desc_res &lt;- cbind(data.frame(Matching = rep(tag, nrow(desc_res))), desc_res)</pre>
+                      <pre class="language-r">#' Generates a `ggplot` histogram of weights. Default is to plot both unscaled and scaled weights on a same graph.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">107</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">292</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    desc_res$Matching[duplicated(desc_res$Matching)] &lt;- ""</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">108</td>
+                    <td class="num">293</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' @param weighted_data object returned after calculating weights using [estimate_weights]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">109</td>
+                    <td class="num">294</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param bin_col a string, color for the bins of histogram</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">110</td>
+                    <td class="num">295</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # output</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">111</td>
-                    <td class="coverage">6<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  desc_res</pre>
+                      <pre class="language-r">#' @param vline_col a string, color for the vertical line in the histogram</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">112</td>
+                    <td class="num">296</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#' @param main_title Name of scaled weights plot and unscaled weights plot, respectively.</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/binary-helper.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">297</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Create pseudo IPD given aggregated binary data</pre>
+                      <pre class="language-r">#' @param bins number of bin parameter to use</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">2</td>
+                    <td class="num">298</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">299</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param binary_agd a data.frame that take different formats depending on \code{format}</pre>
+                      <pre class="language-r">#' @return a plot of unscaled and scaled weights</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">300</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param format a string, "stacked" or "unstacked"</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">5</td>
+                    <td class="num">301</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">6</td>
+                    <td class="num">302</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a data.frame of pseudo binary IPD, with columns USUBJID, ARM, RESPONSE</pre>
+                      <pre class="language-r">plot_weights_ggplot &lt;- function(weighted_data, bin_col, vline_col,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">7</td>
+                    <td class="num">303</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @example inst/examples/get_pseudo_ipd_binary_ex.R</pre>
+                      <pre class="language-r">                                main_title,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">304</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">                                bins) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">9</td>
+                    <td class="num">305</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # check if ggplot2 package is installed</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">10</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">306</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">get_pseudo_ipd_binary &lt;- function(binary_agd, format = c("stacked", "unstacked")) {</pre>
+                      <pre class="language-r">  if (!requireNamespace("ggplot2", quietly = TRUE)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">11</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">307</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # pre check</pre>
+                      <pre class="language-r">    stop("ggplot2 package is needed to run this function")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">12</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">308</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (format == "stacked") {</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">13</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">309</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (!is.data.frame(binary_agd)) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">14</td>
+                    <td class="num">310</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("stacked binary_agd should be data.frame with columns 'ARM', 'RESPONSE', 'COUNT'")</pre>
+                      <pre class="language-r">  weights_stat &lt;- calculate_weights_legend(weighted_data)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">15</td>
+                    <td class="num">311</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">16</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">312</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    names(binary_agd) &lt;- toupper(names(binary_agd))</pre>
+                      <pre class="language-r">  # prepare dataset to use in ggplot</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">17</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">313</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (!all(c("ARM", "RESPONSE", "COUNT") %in% names(binary_agd))) {</pre>
+                      <pre class="language-r">  wt_data0 &lt;- weighted_data$data[, c("weights", "scaled_weights")]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">18</td>
+                    <td class="num">314</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("stacked binary_agd should be data.frame with columns 'ARM', 'Response', 'Count'")</pre>
+                      <pre class="language-r">  colnames(wt_data0) &lt;- main_title</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">19</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">315</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">  wt_data &lt;- stack(wt_data0)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">20</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">316</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (!is.logical(binary_agd$RESPONSE) &amp;&amp; !all(toupper(binary_agd$RESPONSE) %in% c("YES", "NO"))) {</pre>
+                      <pre class="language-r">  wt_data$median &lt;- ifelse(wt_data$ind == main_title[1],</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">21</td>
+                    <td class="num">317</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("'RESPONSE' column in stacked binary_agd should be either logical vector or character vector of 'Yes'/'No'")</pre>
+                      <pre class="language-r">    weights_stat$wt_median, weights_stat$wt_scaled_median</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">22</td>
+                    <td class="num">318</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">23</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">319</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (nrow(binary_agd) %% 2 != 0) {</pre>
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">320</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # create legend data</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">24</td>
+                    <td class="num">321</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("nrow(binary_agd) is not even number, you may miss to provide 1 level of binary response to certain arm")</pre>
+                      <pre class="language-r">  lab &lt;- with(weights_stat, {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">25</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">322</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">    lab &lt;- c(paste0("Median = ", wt_median), paste0("Median = ", wt_scaled_median))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">26</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">323</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else if (format == "unstacked") {</pre>
+                      <pre class="language-r">    lab &lt;- paste0(lab, "\nESS = ", ess, "\nReduction% = ", ess_reduction)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">27</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">324</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (!(is.data.frame(binary_agd) || is.matrix(binary_agd))) {</pre>
+                      <pre class="language-r">    if (nr_na &gt; 0) lab &lt;- paste0(lab, "\n#Missing Weights = ", nr_na)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">28</td>
+                    <td class="num">325</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("unstacked binary_agd should be either a 1x2 or 2x2 data frame or matrix")</pre>
+                      <pre class="language-r">    lab</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">29</td>
+                    <td class="num">326</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">30</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    if (ncol(binary_agd) != 2 || !nrow(binary_agd) %in% c(1, 2)) {</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">31</td>
+                    <td class="num">327</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("unstacked binary_agd should be either a 1x2 or 2x2 data frame or matrix")</pre>
+                      <pre class="language-r">  legend_data &lt;- data.frame(ind = main_title, lab = lab)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">328</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">33</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">329</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bin_res &lt;- toupper(colnames(binary_agd))</pre>
+                      <pre class="language-r">  hist_plot &lt;- ggplot2::ggplot(wt_data) +</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">34</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">330</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    bin_res &lt;- sort(bin_res)</pre>
+                      <pre class="language-r">    ggplot2::geom_histogram(ggplot2::aes_string(x = "values"), bins = bins, color = bin_col, fill = bin_col) +</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">35</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">331</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (!(identical(bin_res, c("FALSE", "TRUE")) || identical(bin_res, c("NO", "YES")))) {</pre>
+                      <pre class="language-r">    ggplot2::geom_vline(ggplot2::aes_string(xintercept = "median"),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">36</td>
+                    <td class="num">332</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("column names of unstacked binary_agd should be either TRUE/FALSE or Yes/No")</pre>
+                      <pre class="language-r">      color = vline_col,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">37</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">333</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">      linetype = "dashed"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">38</td>
+                    <td class="num">334</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    ) +</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">39</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">335</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    ggplot2::theme_bw() +</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">40</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  # pre process binary_agd, depending on format</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">41</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">336</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_binary_agd &lt;- switch(format,</pre>
+                      <pre class="language-r">    ggplot2::facet_wrap(~ind, ncol = 1) +</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">42</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">337</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    "stacked" = {</pre>
+                      <pre class="language-r">    ggplot2::geom_text(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">43</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">338</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      names(binary_agd) &lt;- toupper(names(binary_agd))</pre>
+                      <pre class="language-r">      data = legend_data,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">44</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">339</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (!is.logical(binary_agd$RESPONSE)) {</pre>
+                      <pre class="language-r">      ggplot2::aes_string(label = "lab"), x = Inf, y = Inf, hjust = 1, vjust = 1, size = 3</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">45</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">340</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        binary_agd$RESPONSE &lt;- toupper(binary_agd$RESPONSE)</pre>
+                      <pre class="language-r">    ) +</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">46</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">341</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        binary_agd$RESPONSE &lt;- binary_agd$RESPONSE == "YES"</pre>
+                      <pre class="language-r">    ggplot2::theme(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">47</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">342</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">      axis.title = ggplot2::element_text(size = 12),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">48</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">343</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      binary_agd</pre>
+                      <pre class="language-r">      axis.text = ggplot2::element_text(size = 12)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">49</td>
+                    <td class="num">344</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    },</pre>
+                      <pre class="language-r">    ) +</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">50</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">345</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    "unstacked" = {</pre>
+                      <pre class="language-r">    ggplot2::ylab("Frequency") +</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">51</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">346</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      trt_names &lt;- rownames(binary_agd)</pre>
+                      <pre class="language-r">    ggplot2::xlab("Weight")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">52</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">347</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      bin_res &lt;- toupper(colnames(binary_agd))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">53</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">348</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if ("YES" %in% bin_res) {</pre>
+                      <pre class="language-r">  return(hist_plot)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">54</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">349</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        bin_res &lt;- ifelse(bin_res == "YES", "TRUE", "FALSE")</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">55</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">350</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        colnames(binary_agd) &lt;- bin_res</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">56</td>
+                    <td class="num">351</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">57</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">352</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tmpout &lt;- utils::stack(binary_agd)</pre>
+                      <pre class="language-r">#' Plot method for Estimate Weights objects</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">58</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">353</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tmpout &lt;- cbind(ARM = rep(trt_names, each = 2), tmpout)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">59</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">354</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      names(tmpout) &lt;- c("ARM", "COUNT", "RESPONSE")</pre>
+                      <pre class="language-r">#' The plot function displays individuals weights with key summary in top right legend that includes</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">60</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">355</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      rownames(tmpout) &lt;- NULL</pre>
+                      <pre class="language-r">#' median weight, effective sample size (ESS), and reduction percentage (what percent ESS is reduced from the</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">61</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">356</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tmpout$RESPONSE &lt;- as.logical(tmpout$RESPONSE)</pre>
+                      <pre class="language-r">#' original sample size). There are two options of plotting: base R plot and `ggplot`. The default</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">62</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">357</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tmpout</pre>
+                      <pre class="language-r">#' for base R plot is to plot unscaled and scaled separately. The default</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">63</td>
+                    <td class="num">358</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">#' for `ggplot` is to plot unscaled and scaled weights on a same plot.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">64</td>
+                    <td class="num">359</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">65</td>
+                    <td class="num">360</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param x object from [estimate_weights]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">66</td>
+                    <td class="num">361</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # create pseudo binary IPD</pre>
+                      <pre class="language-r">#' @param ggplot indicator to print base weights plot or `ggplot` weights plot</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">67</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">362</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  use_binary_agd$ARM &lt;- factor(use_binary_agd$ARM, levels = unique(use_binary_agd$ARM))</pre>
+                      <pre class="language-r">#' @param bin_col a string, color for the bins of histogram</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">68</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">363</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  n_per_arm &lt;- tapply(use_binary_agd$COUNT, use_binary_agd$ARM, sum)</pre>
+                      <pre class="language-r">#' @param vline_col a string, color for the vertical line in the histogram</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">69</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">364</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  n_yes_per_arm &lt;- use_binary_agd$COUNT[use_binary_agd$RESPONSE] # use_binary_agd is already ordered as per factor ARM</pre>
+                      <pre class="language-r">#' @param main_title title of the plot. For ggplot, name of scaled weights plot and unscaled weights plot, respectively.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">70</td>
+                    <td class="num">365</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param scaled_weights (base plot only) an indicator for using scaled weights instead of regular weights</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">71</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">366</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tmpipd &lt;- data.frame(</pre>
+                      <pre class="language-r">#' @param bins (`ggplot` only) number of bin parameter to use</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">72</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">367</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    USUBJID = NA,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">73</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">368</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ARM = unlist(</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">74</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">369</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mapply(rep, x = levels(use_binary_agd$ARM), each = n_per_arm, SIMPLIFY = FALSE, USE.NAMES = FALSE)</pre>
+                      <pre class="language-r">#' plot(weighted_sat)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">75</td>
+                    <td class="num">370</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">76</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">371</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    RESPONSE = unlist(</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">77</td>
-                    <td class="coverage">3<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      lapply(seq_along(n_per_arm), function(ii) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">78</td>
-                    <td class="coverage">3<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">        c(rep(TRUE, n_yes_per_arm[ii]), rep(FALSE, n_per_arm[ii] - n_yes_per_arm[ii]))</pre>
+                      <pre class="language-r">#' if (requireNamespace("ggplot2")) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">79</td>
+                    <td class="num">372</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      })</pre>
+                      <pre class="language-r">#'   plot(weighted_sat, ggplot = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">80</td>
+                    <td class="num">373</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">81</td>
+                    <td class="num">374</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">82</td>
-                    <td class="coverage">3<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  tmpipd$USUBJID &lt;- paste0("pseudo_binary_subj_", seq_len(nrow(tmpipd)))</pre>
+                      <pre class="language-r">#' @describeIn estimate_weights Plot method for estimate_weights objects</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">83</td>
+                    <td class="num">375</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">84</td>
+                    <td class="num">376</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # output</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">85</td>
-                    <td class="coverage">3<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  tmpipd</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">86</td>
+                    <td class="num">377</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">plot.maicplus_estimate_weights &lt;- function(x, ggplot = FALSE,</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/bucher.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">378</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Bucher method for combining treatment effects</pre>
+                      <pre class="language-r">                                           bin_col = "#6ECEB2", vline_col = "#688CE8",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">2</td>
+                    <td class="num">379</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                                           main_title = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">380</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Given two treatment effects of A vs. C and B vs. C</pre>
+                      <pre class="language-r">                                           scaled_weights = TRUE,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">381</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' derive the treatment effects of A vs. B using the Bucher method.</pre>
+                      <pre class="language-r">                                           bins = 50, ...) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">5</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">382</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Two-sided confidence interval and Z-test p-value are also calculated.</pre>
+                      <pre class="language-r">  if (ggplot) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">6</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">383</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Treatment effects and standard errors should be in log scale</pre>
+                      <pre class="language-r">    if (is.null(main_title)) main_title &lt;- c("Scaled Individual Weights", "Unscaled Individual Weights")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">384</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' for hazard ratio, odds ratio, and risk ratio.</pre>
+                      <pre class="language-r">    plot_weights_ggplot(x, bin_col, vline_col, main_title, bins)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">385</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Treatment effects and standard errors should be in natural scale</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">9</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">386</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' for risk difference and mean difference.</pre>
+                      <pre class="language-r">    if (is.null(main_title)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">10</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">387</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      main_title &lt;- ifelse(scaled_weights, "Scaled Individual Weights", "Unscaled Individual Weights")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">11</td>
+                    <td class="num">388</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt a list of two scalars for the study with the</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">389</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' experimental arm. `'est'` is the point estimate and `'se'`</pre>
+                      <pre class="language-r">    plot_weights_base(x, bin_col, vline_col, main_title, scaled_weights)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">13</td>
+                    <td class="num">390</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' is the standard error of the treatment effect.</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">14</td>
+                    <td class="num">391</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' For time-to-event data, `'est'` and `'se'` should be point estimate and</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">15</td>
+                    <td class="num">392</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' standard error of the log hazard ratio.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">16</td>
+                    <td class="num">393</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' For binary data, `'est'` and `'se'` should be point estimate and</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">17</td>
+                    <td class="num">394</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' standard error of the log odds ratio, log risk ratio, or risk</pre>
+                      <pre class="language-r">#' Check to see if weights are optimized correctly</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">18</td>
+                    <td class="num">395</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' difference.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">19</td>
+                    <td class="num">396</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' For continuous data,  `'est'` and `'se'` should be point estimate and</pre>
+                      <pre class="language-r">#' This function checks to see if the optimization is done properly by checking the covariate averages</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">20</td>
+                    <td class="num">397</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' standard error of the mean difference.</pre>
+                      <pre class="language-r">#' before and after adjustment.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">21</td>
+                    <td class="num">398</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param com same as \code{trt}, but for the study with the</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">22</td>
+                    <td class="num">399</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' control arm</pre>
+                      <pre class="language-r">#' @param weighted_data object returned after calculating weights using \code{\link{estimate_weights}}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">23</td>
+                    <td class="num">400</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param conf_lv a numerical scalar, prescribe confidence level to derive</pre>
+                      <pre class="language-r">#' @param processed_agd a data frame, object returned after using \code{\link{process_agd}} or</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">24</td>
+                    <td class="num">401</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' two-sided confidence interval for the treatment effect</pre>
+                      <pre class="language-r">#' aggregated data following the same naming convention</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">25</td>
+                    <td class="num">402</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">403</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a list with 5 elements,</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">404</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' \describe{</pre>
+                      <pre class="language-r">#' check_weights(weighted_sat, process_agd(agd))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">28</td>
+                    <td class="num">405</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{est}{a scalar, point estimate of the treatment effect}</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">29</td>
+                    <td class="num">406</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{se}{a scalar, standard error of the treatment effect}</pre>
+                      <pre class="language-r">#' @import DescTools</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">30</td>
+                    <td class="num">407</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{ci_l}{a scalar, lower confidence limit of a two-sided CI</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">31</td>
+                    <td class="num">408</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   with prescribed nominal level by \code{conf_lv}}</pre>
+                      <pre class="language-r">#' @return data.frame of weighted and unweighted covariate averages of the IPD,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">409</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{ci_u}{a scalar, upper confidence limit of a two-sided CI</pre>
+                      <pre class="language-r">#' average of aggregate data, and sum of inner products of covariate \eqn{x_i} and the weights (\eqn{exp(x_i\beta)})</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">33</td>
+                    <td class="num">410</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   with prescribed nominal level by \code{conf_lv}}</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">34</td>
+                    <td class="num">411</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{pval}{p-value of Z-test, with null hypothesis that</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">35</td>
+                    <td class="num">412</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \code{est} is zero}</pre>
+                      <pre class="language-r">check_weights &lt;- function(weighted_data, processed_agd) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">36</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">413</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">  ipd_with_weights &lt;- weighted_data$data</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">37</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">414</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">  match_cov &lt;- weighted_data$centered_colnames</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">38</td>
+                    <td class="num">415</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">39</td>
+                    <td class="num">416</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' trt &lt;- list(est = log(1.1), se = 0.2)</pre>
+                      <pre class="language-r">  # if algorithm is correct, all centered columns should have a weighted summation to a very small number around zero</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">40</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">417</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' com &lt;- list(est = log(1.3), se = 0.18)</pre>
+                      <pre class="language-r">  num_check &lt;- ipd_with_weights$weights %*% as.matrix(ipd_with_weights[, match_cov, drop = FALSE])</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">41</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">418</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' result &lt;- bucher(trt, com, conf_lv = 0.9)</pre>
+                      <pre class="language-r">  num_check &lt;- round(num_check, 4)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">42</td>
+                    <td class="num">419</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' print(result, ci_digits = 3, pval_digits = 3)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">43</td>
+                    <td class="num">420</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">bucher &lt;- function(trt, com, conf_lv = 0.95) {</pre>
+                      <pre class="language-r">  # for reporting</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">44</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">421</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!isTRUE(is.finite(trt$est))) stop("trt$est is not valid: ", trt$est)</pre>
+                      <pre class="language-r">  outdata &lt;- data.frame(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">45</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">422</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!isTRUE(is.finite(trt$se))) stop("trt$se is not valid: ", trt$se)</pre>
+                      <pre class="language-r">    covariate = gsub("_CENTERED$", "", match_cov),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">46</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">423</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!isTRUE(is.finite(com$est))) stop("com$est is not valid: ", com$est)</pre>
+                      <pre class="language-r">    match_stat = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">47</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">424</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!isTRUE(is.finite(com$se))) stop("com$se is not valid: ", com$se)</pre>
+                      <pre class="language-r">    internal_trial = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">48</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">425</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (conf_lv &lt; 0 || 1 &lt; conf_lv) stop("conf_lv must be in (0, 1): ", conf_lv)</pre>
+                      <pre class="language-r">    internal_trial_after_weighted = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">49</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">426</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    external_trial = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">50</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">427</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  est &lt;- trt$est - com$est</pre>
+                      <pre class="language-r">    sum_centered_IPD_with_weights = as.vector(num_check)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">51</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">428</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  se &lt;- sqrt(trt$se^2 + com$se^2)</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">52</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">429</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ci_l &lt;- est - stats::qnorm(0.5 + conf_lv / 2) * se</pre>
+                      <pre class="language-r">  attr(outdata, "footer") &lt;- list()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">53</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">430</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ci_u &lt;- est + stats::qnorm(0.5 + conf_lv / 2) * se</pre>
+                      <pre class="language-r">  # find item that was matched by mean</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">54</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">431</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (est &gt; 0) {</pre>
+                      <pre class="language-r">  ind_mean &lt;- lapply(outdata$covariate, grep, x = names(processed_agd), value = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">55</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">432</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pval &lt;- 2 * (1 - stats::pnorm(est, 0, se))</pre>
+                      <pre class="language-r">  ind_mean &lt;- sapply(ind_mean, function(ii) any(grepl("_MEAN$", ii)))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">56</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">433</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">  outdata$match_stat &lt;- ifelse(grepl("_MEDIAN$", outdata$covariate), "Median",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">57</td>
-                    <td class="coverage">10<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">434</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pval &lt;- 2 * stats::pnorm(est, 0, se)</pre>
+                      <pre class="language-r">    ifelse(grepl("_SQUARED$", outdata$covariate), "SD",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">58</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">435</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">      ifelse(ind_mean, "Mean", "Prop")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">59</td>
+                    <td class="num">436</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">60</td>
-                    <td class="coverage">11<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  outdata &lt;- list(</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">61</td>
-                    <td class="coverage">11<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    est = est,</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">62</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">437</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    se = se,</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">63</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">438</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ci_l = ci_l,</pre>
+                      <pre class="language-r">  outdata$covariate &lt;- gsub("_MEDIAN|_SQUARED", "", outdata$covariate)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">64</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">439</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ci_u = ci_u,</pre>
+                      <pre class="language-r">  # fill in corresponding agd data</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">65</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">440</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pval = pval</pre>
+                      <pre class="language-r">  outdata$external_trial &lt;- unlist(processed_agd[paste(outdata$covariate, toupper(outdata$match_stat), sep = "_")])</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">66</td>
+                    <td class="num">441</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">67</td>
+                    <td class="num">442</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # fill in stat from unweighted and weighted IPD</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">68</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">443</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  class(outdata) &lt;- c("maicplus_bucher", "list")</pre>
+                      <pre class="language-r">  for (ii in seq_len(nrow(outdata))) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">69</td>
-                    <td class="coverage">11<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">444</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  outdata</pre>
+                      <pre class="language-r">    covname &lt;- outdata$covariate[ii]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">70</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">445</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">    if (outdata$match_stat[ii] %in% c("Mean", "Prop")) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">71</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">446</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      outdata$internal_trial[ii] &lt;- mean(ipd_with_weights[[covname]], na.rm = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">72</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">447</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      outdata$internal_trial_after_weighted[ii] &lt;- weighted.mean(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">73</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">448</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Calculate standard error from the reported confidence interval.</pre>
+                      <pre class="language-r">        ipd_with_weights[[covname]],</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">74</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">449</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        w = ipd_with_weights$weights, na.rm = TRUE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">75</td>
+                    <td class="num">450</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Comparator studies often only report confidence interval of the</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">76</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#' treatment effects. This function calculates standard error of the</pre>
+                  <tr class="missed">
+                    <td class="num">451</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    } else if (outdata$match_stat[ii] == "Median") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">77</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">452</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' treatment effect given the reported confidence interval.</pre>
+                      <pre class="language-r">      outdata$internal_trial[ii] &lt;- quantile(ipd_with_weights[[covname]],</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">78</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">453</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' For relative treatment effect (i.e. hazard ratio, odds ratio, and</pre>
+                      <pre class="language-r">        probs = 0.5,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">79</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">454</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' risk ratio), the function would log the confidence interval.</pre>
+                      <pre class="language-r">        na.rm = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">80</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">455</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' For risk difference and mean difference,</pre>
+                      <pre class="language-r">        type = 2,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">81</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">456</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' we do not log the confidence interval.</pre>
+                      <pre class="language-r">        names = FALSE</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">82</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">457</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' The option to log the confidence interval is controlled</pre>
+                      <pre class="language-r">      ) # SAS default</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">83</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">458</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' by `'logged'` parameter.</pre>
+                      <pre class="language-r">      outdata$internal_trial_after_weighted[ii] &lt;- DescTools::Quantile(ipd_with_weights[[covname]],</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">84</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">459</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        weights = ipd_with_weights$weights,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">85</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">460</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param CI_lower Reported lower percentile value of the</pre>
+                      <pre class="language-r">        probs = 0.5,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">86</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">461</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' treatment effect</pre>
+                      <pre class="language-r">        na.rm = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">87</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">462</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param CI_upper Reported upper percentile value of the</pre>
+                      <pre class="language-r">        type = 5,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">88</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">463</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' treatment effect</pre>
+                      <pre class="language-r">        names = FALSE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">89</td>
+                    <td class="num">464</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param CI_perc Percentage of confidence interval reported</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">90</td>
+                    <td class="num">465</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param logged Whether the confidence interval should be logged.</pre>
+                      <pre class="language-r">      # no IPD equals to reported AgD median</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">91</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">466</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' For relative treatment effect, log should be applied because</pre>
+                      <pre class="language-r">      msg_ind &lt;- !any(ipd_with_weights[[covname]] == outdata$external_trial[ii], na.rm = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">92</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">467</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' estimated log treatment effect is approximately normally distributed.</pre>
+                      <pre class="language-r">      if (msg_ind) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">93</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">468</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Standard error of log relative treatment effect if `'logged'`</pre>
+                      <pre class="language-r">        msg_txt &lt;- paste0(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">94</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">469</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' is true and standard error of the treatment effect if `'logged'`</pre>
+                      <pre class="language-r">          "For covariate ", covname, ", it was matched to AgD median, but there is no IPD identical to AgD median,",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">95</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">470</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' is false</pre>
+                      <pre class="language-r">          "hence median after weighted will not equal to AgD median exactly."</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">96</td>
+                    <td class="num">471</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">97</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">472</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' find_SE_from_CI(CI_lower = 0.55, CI_upper = 0.90, CI_perc = 0.95)</pre>
+                      <pre class="language-r">        attr(outdata, "footer") &lt;- c(attr(outdata, "footer"), msg_txt)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">98</td>
+                    <td class="num">473</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">99</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">474</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    } else if (outdata$match_stat[ii] == "SD") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">100</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">475</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">find_SE_from_CI &lt;- function(CI_lower = NULL, CI_upper = NULL,</pre>
+                      <pre class="language-r">      outdata$internal_trial[ii] &lt;- sd(ipd_with_weights[[covname]], na.rm = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">101</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">476</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            CI_perc = 0.95, logged = TRUE) {</pre>
+                      <pre class="language-r">      wm_squared &lt;- weighted.mean(ipd_with_weights[[covname]]^2, w = ipd_with_weights$weights, na.rm = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">102</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">477</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (CI_perc &gt; 1 || CI_perc &lt; 0) {</pre>
+                      <pre class="language-r">      ms_agd &lt;- processed_agd[[paste0(outdata$covariate[ii], "_MEAN")]]^2</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">103</td>
+                    <td class="num">478</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("CI_perc has to be between 0 and 1")</pre>
+                      <pre class="language-r">      outdata$internal_trial_after_weighted[ii] &lt;- sqrt(wm_squared - ms_agd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">104</td>
+                    <td class="num">479</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">105</td>
+                    <td class="num">480</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">106</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(CI_lower) || is.null(CI_upper)) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">107</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    stop("Both CI_lower and CI_upper need to be specified")</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">108</td>
+                    <td class="num">481</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">109</td>
+                    <td class="num">482</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # output</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">110</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">483</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!is.numeric(CI_lower) || !is.numeric(CI_upper)) {</pre>
+                      <pre class="language-r">  class(outdata) &lt;- c("maicplus_check_weights", "data.frame")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">111</td>
+                    <td class="num">484</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("Both CI_lower and CI_upper need to be specified")</pre>
+                      <pre class="language-r">  outdata</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">112</td>
+                    <td class="num">485</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">113</td>
+                    <td class="num">486</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">114</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">487</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  alpha &lt;- 1 - CI_perc</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">115</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">488</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  se &lt;- ifelse(logged,</pre>
+                      <pre class="language-r">#' Print method for Check Weights objects</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">116</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">489</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    (log(CI_upper) - log(CI_lower)) / (2 * qnorm(1 - alpha / 2)),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">117</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">490</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    (CI_upper - CI_lower) / (2 * qnorm(1 - alpha / 2))</pre>
+                      <pre class="language-r">#' @param x object from [check_weights]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">118</td>
+                    <td class="num">491</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#' @param mean_digits number of digits for rounding mean columns in the output</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">119</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">492</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  return(se)</pre>
+                      <pre class="language-r">#' @param prop_digits number of digits for rounding proportion columns in the output</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">120</td>
+                    <td class="num">493</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#' @param sd_digits number of digits for rounding mean columns in the output</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">121</td>
+                    <td class="num">494</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param digits minimal number of significant digits, see [print.default].</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">122</td>
+                    <td class="num">495</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Print method for `maicplus_bucher` object</pre>
+                      <pre class="language-r">#' @param ... further arguments to [print.data.frame]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">123</td>
+                    <td class="num">496</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @describeIn check_weights Print method for check_weights objects</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">124</td>
+                    <td class="num">497</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param x `maicplus_bucher` object</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">125</td>
+                    <td class="num">498</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ci_digits an integer, number of decimal places for point</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">126</td>
+                    <td class="num">499</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' estimate and derived confidence limits</pre>
+                      <pre class="language-r">print.maicplus_check_weights &lt;- function(x,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">127</td>
+                    <td class="num">500</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param pval_digits an integer, number of decimal places to display</pre>
+                      <pre class="language-r">                                         mean_digits = 2,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">128</td>
+                    <td class="num">501</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Z-test p-value</pre>
+                      <pre class="language-r">                                         prop_digits = 2,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">129</td>
+                    <td class="num">502</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param exponentiate whether the treatment effect and confidence</pre>
+                      <pre class="language-r">                                         sd_digits = 3,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">130</td>
+                    <td class="num">503</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' interval should be exponentiated. This applies to relative</pre>
+                      <pre class="language-r">                                         digits = getOption("digits"), ...) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">131</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">504</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' treatment effects. Default is set to false.</pre>
+                      <pre class="language-r">  round_digits &lt;- c("Mean" = mean_digits, "Prop" = prop_digits, "SD" = sd_digits)[x$match_stat]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">132</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">505</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ... not used</pre>
+                      <pre class="language-r">  round_digits[is.na(round_digits)] &lt;- digits</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">133</td>
+                    <td class="num">506</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn bucher Print method for `maicplus_bucher` objects</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">134</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">507</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">  x$external_trial &lt;- round(x$external_trial, round_digits)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">135</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">508</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  x$internal_trial &lt;- round(x$internal_trial, round_digits)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">136</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">509</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">print.maicplus_bucher &lt;- function(x, ci_digits = 2, pval_digits = 3,</pre>
+                      <pre class="language-r">  x$internal_trial_after_weighted &lt;- round(x$internal_trial_after_weighted, round_digits)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">137</td>
+                    <td class="num">510</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                  exponentiate = FALSE, ...) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">138</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">511</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  transform_this &lt;- function(x) {</pre>
+                      <pre class="language-r">  print.data.frame(x, ...)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">139</td>
-                    <td class="coverage">12<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">512</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ifelse(exponentiate, exp(x), x)</pre>
+                      <pre class="language-r">  footer &lt;- unlist(attr(x, "footer"))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">140</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">513</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  if (length(footer)) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">141</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">514</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  a &lt;- format(round(transform_this(x$est), ci_digits),</pre>
+                      <pre class="language-r">    cat("\n")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">142</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">515</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    nsmall = ci_digits</pre>
+                      <pre class="language-r">    for (f in seq_along(footer)) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">516</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      cat(paste0("[", f, "] ", footer[f]))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">143</td>
+                    <td class="num">517</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">144</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">518</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  b &lt;- format(round(transform_this(x$ci_l), ci_digits),</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">145</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">519</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    nsmall = ci_digits</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">146</td>
+                    <td class="num">520</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">147</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">521</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  c &lt;- format(round(transform_this(x$ci_u), ci_digits),</pre>
+                      <pre class="language-r">#' Note on Expected Sample Size Reduction</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">148</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">522</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    nsmall = ci_digits</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">149</td>
+                    <td class="num">523</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#' @param width Number of characters to break string into new lines (`\n`).</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">150</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">524</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res &lt;- paste0(a, " [", b, "; ", c, "]")</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">151</td>
+                    <td class="num">525</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @return A character string</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">152</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">526</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  disp_pval &lt;- round(x$pval, pval_digits)</pre>
+                      <pre class="language-r">#' @keywords internal</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">153</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">527</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  disp_pval &lt;-</pre>
+                      <pre class="language-r">ess_footnote_text &lt;- function(width = 0.9 * getOption("width")) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">154</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">528</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ifelse(disp_pval == 0,</pre>
+                      <pre class="language-r">  text &lt;- "An ESS reduction up to ~60% is not unexpected based on the 2021 survey of NICE's technology appraisals</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">155</td>
-                    <td class="coverage">4<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      paste0("&lt;", 1 / (10^pval_digits)),</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">156</td>
-                    <td class="coverage">4<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      format(disp_pval, nsmall = pval_digits)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">157</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">158</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">159</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">529</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  output &lt;- c(res, disp_pval)</pre>
+                      <pre class="language-r">(https://onlinelibrary.wiley.com/doi/full/10.1002/jrsm.1511), whereas a reduction of &gt;75% is less common</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">160</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">530</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(output) &lt;- c("result", "pvalue")</pre>
+                      <pre class="language-r">and it may be considered suboptimal."</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">161</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">531</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  print(output)</pre>
+                      <pre class="language-r">  paste0(strwrap(text, width = width), collapse = "\n")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">162</td>
+                    <td class="num">532</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
@@ -10124,2762 +9951,2776 @@ <h2>maicplus coverage - 54.75%</h2>
                     <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @importFrom survival survfit Surv</pre>
+                      <pre class="language-r">#' @importFrom survival survfit Surv coxph</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return A list, contains 'descriptive' and 'inferential'</pre>
+                      <pre class="language-r">#' @importFrom lmtest coeftest coefci</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' @importFrom sandwich vcovHC</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @importFrom boot boot boot.ci</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">maic_unanchored &lt;- function(weights_object,</pre>
+                      <pre class="language-r">#' @return A list, contains 'descriptive' and 'inferential'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            ipd,</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">42</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            pseudo_ipd,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">43</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            trt_ipd,</pre>
+                      <pre class="language-r">maic_unanchored &lt;- function(weights_object,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">44</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            trt_agd,</pre>
+                      <pre class="language-r">                            ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">45</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            trt_var_ipd = "ARM",</pre>
+                      <pre class="language-r">                            pseudo_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">46</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            trt_var_agd = "ARM",</pre>
+                      <pre class="language-r">                            trt_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            endpoint_type = "tte",</pre>
+                      <pre class="language-r">                            trt_agd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">48</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            endpoint_name = "Time to Event Endpoint",</pre>
+                      <pre class="language-r">                            trt_var_ipd = "ARM",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">49</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            eff_measure = c("HR", "OR", "RR", "RD"),</pre>
+                      <pre class="language-r">                            trt_var_agd = "ARM",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">50</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            boot_ci_type = c("norm", "basic", "stud", "perc", "bca"),</pre>
+                      <pre class="language-r">                            endpoint_type = "tte",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">51</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            # time to event specific args</pre>
+                      <pre class="language-r">                            endpoint_name = "Time to Event Endpoint",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">52</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            time_scale = "months",</pre>
+                      <pre class="language-r">                            eff_measure = c("HR", "OR", "RR", "RD"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">53</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            km_conf_type = "log-log",</pre>
+                      <pre class="language-r">                            boot_ci_type = c("norm", "basic", "stud", "perc", "bca"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            # binary specific args</pre>
+                      <pre class="language-r">                            # time to event specific args</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">55</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            binary_robust_cov_type = "HC3") {</pre>
+                      <pre class="language-r">                            time_scale = "months",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # ==&gt; Initial Setup ------------------------------------------</pre>
+                      <pre class="language-r">                            km_conf_type = "log-log",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">57</td>
                     <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                            # binary specific args</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">58</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                            binary_robust_cov_type = "HC3") {</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">59</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # ==&gt; Initial Setup ------------------------------------------</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">60</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # ~~~ Create the hull for the output from this function</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">58</td>
+                    <td class="num">61</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">59</td>
+                    <td class="num">62</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    descriptive = list(),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">60</td>
+                    <td class="num">63</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    inferential = list()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">61</td>
+                    <td class="num">64</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">62</td>
+                    <td class="num">65</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">63</td>
+                    <td class="num">66</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res_AB &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">64</td>
+                    <td class="num">67</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    est = NA,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">65</td>
+                    <td class="num">68</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    se = NA,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">66</td>
+                    <td class="num">69</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    ci_l = NA,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">67</td>
+                    <td class="num">70</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    ci_u = NA,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">68</td>
+                    <td class="num">71</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    pval = NA</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">69</td>
+                    <td class="num">72</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">70</td>
+                    <td class="num">73</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">71</td>
+                    <td class="num">74</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # ~~~ Initial colname process and precheck on effect measure</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">72</td>
+                    <td class="num">75</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  names(ipd) &lt;- toupper(names(ipd))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">73</td>
+                    <td class="num">76</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  names(pseudo_ipd) &lt;- toupper(names(pseudo_ipd))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">74</td>
+                    <td class="num">77</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  trt_var_ipd &lt;- toupper(trt_var_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">75</td>
+                    <td class="num">78</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  trt_var_agd &lt;- toupper(trt_var_agd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">76</td>
+                    <td class="num">79</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">77</td>
+                    <td class="num">80</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (length(eff_measure) &gt; 1) eff_measure &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">78</td>
+                    <td class="num">81</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (is.null(eff_measure)) eff_measure &lt;- list(binary = "OR", tte = "HR")[[endpoint_type]]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">79</td>
+                    <td class="num">82</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">80</td>
+                    <td class="num">83</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # ~~~ Setup ARM column and make related pre-checks</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">81</td>
+                    <td class="num">84</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!trt_var_ipd %in% names(ipd)) stop("cannot find arm indicator column trt_var_ipd in ipd")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">82</td>
+                    <td class="num">85</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!trt_var_agd %in% names(pseudo_ipd)) stop("cannot find arm indicator column trt_var_agd in pseudo_ipd")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">83</td>
+                    <td class="num">86</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (trt_var_ipd != "ARM") ipd$ARM &lt;- ipd[[trt_var_ipd]]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">84</td>
+                    <td class="num">87</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (trt_var_agd != "ARM") pseudo_ipd$ARM &lt;- pseudo_ipd[[trt_var_agd]]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">85</td>
+                    <td class="num">88</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  ipd$ARM &lt;- as.character(ipd$ARM) # just to avoid potential error when merging</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">86</td>
+                    <td class="num">89</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  pseudo_ipd$ARM &lt;- as.character(pseudo_ipd$ARM) # just to avoid potential error when merging</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">87</td>
+                    <td class="num">90</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!trt_ipd %in% ipd$ARM) stop("trt_ipd does not exist in ipd$ARM")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">88</td>
+                    <td class="num">91</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!trt_agd %in% pseudo_ipd$ARM) stop("trt_agd does not exist in pseudo_ipd$ARM")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">89</td>
+                    <td class="num">92</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">90</td>
+                    <td class="num">93</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # ~~~ More pre-checks</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">91</td>
+                    <td class="num">94</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  endpoint_type &lt;- match.arg(endpoint_type, c("binary", "tte"))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">92</td>
+                    <td class="num">95</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!"maicplus_estimate_weights" %in% class(weights_object)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">93</td>
+                    <td class="num">96</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    stop("weights_object should be an object returned by estimate_weights")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">94</td>
+                    <td class="num">97</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">95</td>
+                    <td class="num">98</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (any(duplicated(ipd$USUBJID))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">96</td>
+                    <td class="num">99</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    warning(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">97</td>
+                    <td class="num">100</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "check your ipd, it has duplicated usubjid, this indicates, ",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">98</td>
+                    <td class="num">101</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "it might contain multiple endpoints for each subject"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">99</td>
+                    <td class="num">102</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">100</td>
+                    <td class="num">103</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">101</td>
+                    <td class="num">104</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!all(ipd$USUBJID %in% weights_object$data$USUBJID)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">102</td>
+                    <td class="num">105</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    stop(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">103</td>
+                    <td class="num">106</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "These pts in ipd cannot be found in weights_object ",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">104</td>
+                    <td class="num">107</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">      toString(setdiff(ipd$USUBJID, weights_object$USUBJID))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">105</td>
+                    <td class="num">108</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">106</td>
+                    <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">107</td>
+                    <td class="num">110</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  time_scale &lt;- match.arg(arg = time_scale, choices = c("days", "weeks", "months", "years"))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">108</td>
+                    <td class="num">111</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (endpoint_type == "binary") { # for binary effect measure</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">109</td>
+                    <td class="num">112</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">110</td>
+                    <td class="num">113</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    if (any(!c("USUBJID", "RESPONSE") %in% names(ipd))) stop("ipd should have 'USUBJID', 'RESPONSE' columns at minimum")</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">111</td>
+                    <td class="num">114</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    eff_measure &lt;- match.arg(eff_measure, choices = c("OR", "RD", "RR"), several.ok = FALSE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">112</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
                   <tr class="covered">
-                    <td class="num">113</td>
+                    <td class="num">115</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    binary_robust_cov_type &lt;- match.arg(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">114</td>
+                    <td class="num">116</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      binary_robust_cov_type,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">115</td>
+                    <td class="num">117</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      choices = c("HC3", "const", "HC", "HC0", "HC1", "HC2", "HC4", "HC4m", "HC5")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">116</td>
+                    <td class="num">118</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">117</td>
+                    <td class="num">119</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  } else if (endpoint_type == "tte") { # for time to event effect measure</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">118</td>
+                    <td class="num">120</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">119</td>
+                    <td class="num">121</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    if (!all(c("USUBJID", "TIME", "EVENT", trt_var_ipd) %in% names(ipd))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">120</td>
+                    <td class="num">122</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">      stop("ipd needs to include at least USUBJID, TIME, EVENT, ", trt_var_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">121</td>
+                    <td class="num">123</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">122</td>
+                    <td class="num">124</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    if (!all(c("TIME", "EVENT", trt_var_agd) %in% names(pseudo_ipd))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">123</td>
+                    <td class="num">125</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">      stop("pseudo_ipd needs to include at least TIME, EVENT, ", trt_var_agd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">124</td>
+                    <td class="num">126</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">125</td>
+                    <td class="num">127</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    eff_measure &lt;- match.arg(eff_measure, choices = c("HR"), several.ok = FALSE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">126</td>
+                    <td class="num">128</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">127</td>
+                    <td class="num">129</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  boot_ci_type &lt;- match.arg(boot_ci_type)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">128</td>
+                    <td class="num">130</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">129</td>
+                    <td class="num">131</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # ==&gt; IPD and AgD data preparation ------------------------------------------</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">130</td>
+                    <td class="num">132</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : subset ipd, retain only ipd from interested trts</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">131</td>
+                    <td class="num">133</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  ipd &lt;- ipd[ipd$ARM == trt_ipd, , drop = TRUE]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">132</td>
+                    <td class="num">134</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  pseudo_ipd &lt;- pseudo_ipd[pseudo_ipd$ARM == trt_agd, , drop = TRUE]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">133</td>
+                    <td class="num">135</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">134</td>
+                    <td class="num">136</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : assign weights to real and pseudo ipd</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">135</td>
+                    <td class="num">137</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  ipd$weights &lt;- weights_object$data$weights[match(weights_object$data$USUBJID, ipd$USUBJID)]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">136</td>
+                    <td class="num">138</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  pseudo_ipd$weights &lt;- 1</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">137</td>
+                    <td class="num">139</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">138</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : necessary formatting for pseudo ipd</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">139</td>
+                    <td class="num">141</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!"USUBJID" %in% names(pseudo_ipd)) pseudo_ipd$USUBJID &lt;- paste0("ID", seq_len(nrow(pseudo_ipd)))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">140</td>
+                    <td class="num">142</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if ("RESPONSE" %in% names(pseudo_ipd) &amp;&amp; is.logical(pseudo_ipd$RESPONSE)) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">141</td>
+                    <td class="num">143</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    pseudo_ipd$RESPONSE &lt;- as.numeric(pseudo_ipd$RESPONSE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">142</td>
+                    <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">143</td>
+                    <td class="num">145</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">144</td>
+                    <td class="num">146</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : give warning when individual pts in IPD has no weights</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">145</td>
+                    <td class="num">147</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (any(is.na(ipd$weights))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">146</td>
+                    <td class="num">148</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    ipd &lt;- ipd[!is.na(ipd$weights), , drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">147</td>
+                    <td class="num">149</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    warning(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">148</td>
+                    <td class="num">150</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">      paste(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">149</td>
+                    <td class="num">151</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        "these usubjid in ipd have no weight in weights_object, and hence excluded from analysis:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">150</td>
+                    <td class="num">152</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        paste(ipd$USUBJID[is.na(ipd$weights)], collapse = ",")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">151</td>
+                    <td class="num">153</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">152</td>
+                    <td class="num">154</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">153</td>
+                    <td class="num">155</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    if (nrow(ipd) == 0) stop("there is no pts with weight in IPD!!")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">154</td>
+                    <td class="num">156</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">155</td>
+                    <td class="num">157</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">156</td>
+                    <td class="num">158</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : retain necessary columns</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">157</td>
+                    <td class="num">159</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (endpoint_type == "tte") {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">158</td>
+                    <td class="num">160</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    retain_cols &lt;- c("USUBJID", "ARM", "TIME", "EVENT", "weights")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">159</td>
+                    <td class="num">161</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">160</td>
+                    <td class="num">162</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    retain_cols &lt;- c("USUBJID", "ARM", "RESPONSE", "weights")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">161</td>
+                    <td class="num">163</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">162</td>
+                    <td class="num">164</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  ipd &lt;- ipd[, retain_cols, drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">163</td>
+                    <td class="num">165</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  pseudo_ipd &lt;- pseudo_ipd[, retain_cols, drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">164</td>
+                    <td class="num">166</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">165</td>
+                    <td class="num">167</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : merge real and pseudo ipds</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">166</td>
+                    <td class="num">168</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  dat &lt;- rbind(ipd, pseudo_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">167</td>
+                    <td class="num">169</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  dat$ARM &lt;- factor(dat$ARM, levels = c(trt_agd, trt_ipd))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">168</td>
+                    <td class="num">170</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">169</td>
+                    <td class="num">171</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # ==&gt; Inferential output ------------------------------------------</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">170</td>
+                    <td class="num">172</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">171</td>
+                    <td class="num">173</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  result &lt;- if (endpoint_type == "tte") {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">172</td>
+                    <td class="num">174</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    maic_unanchored_tte(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">173</td>
+                    <td class="num">175</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      res, res_AB, dat, ipd, pseudo_ipd, km_conf_type, time_scale,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">174</td>
+                    <td class="num">176</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      weights_object, endpoint_name, boot_ci_type, trt_ipd, trt_agd</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">175</td>
+                    <td class="num">177</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">176</td>
+                    <td class="num">178</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  } else if (endpoint_type == "binary") {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">177</td>
+                    <td class="num">179</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    maic_unanchored_binary(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">178</td>
+                    <td class="num">180</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      res, res_AB, dat, ipd, pseudo_ipd, binary_robust_cov_type,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">179</td>
+                    <td class="num">181</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      weights_object, endpoint_name, eff_measure, boot_ci_type, trt_ipd, trt_agd</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">180</td>
+                    <td class="num">182</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">181</td>
+                    <td class="num">183</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">182</td>
+                    <td class="num">184</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    stop("Endpoint type ", endpoint_type, " currently unsupported.")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">183</td>
+                    <td class="num">185</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">184</td>
+                    <td class="num">186</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">185</td>
+                    <td class="num">187</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # output</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">186</td>
+                    <td class="num">188</td>
                     <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  result</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">187</td>
+                    <td class="num">189</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">188</td>
+                    <td class="num">190</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">189</td>
+                    <td class="num">191</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"># MAIC inference functions for TTE outcome type ------------</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">190</td>
+                    <td class="num">192</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">191</td>
+                    <td class="num">193</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">maic_unanchored_tte &lt;- function(res,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">192</td>
+                    <td class="num">194</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                res_AB,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">193</td>
+                    <td class="num">195</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                dat,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">194</td>
+                    <td class="num">196</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">195</td>
+                    <td class="num">197</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                pseudo_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">196</td>
+                    <td class="num">198</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                km_conf_type,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">197</td>
+                    <td class="num">199</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                time_scale,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">198</td>
+                    <td class="num">200</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                weights_object,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">199</td>
+                    <td class="num">201</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                endpoint_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">200</td>
+                    <td class="num">202</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                boot_ci_type,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">201</td>
+                    <td class="num">203</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                trt_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">202</td>
+                    <td class="num">204</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                trt_agd) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">203</td>
+                    <td class="num">205</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # ~~~ Descriptive table before and after matching</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">204</td>
+                    <td class="num">206</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : derive km w and w/o weights</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">205</td>
+                    <td class="num">207</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  kmobj_dat &lt;- survfit(Surv(TIME, EVENT) ~ ARM, dat, conf.type = km_conf_type)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">206</td>
+                    <td class="num">208</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  kmobj_dat_adj &lt;- survfit(Surv(TIME, EVENT) ~ ARM, dat, weights = dat$weights, conf.type = km_conf_type)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">207</td>
+                    <td class="num">209</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res$descriptive[["survfit_before"]] &lt;- survfit_makeup(kmobj_dat)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">208</td>
+                    <td class="num">210</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res$descriptive[["survfit_after"]] &lt;- survfit_makeup(kmobj_dat_adj)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">209</td>
+                    <td class="num">211</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : derive median survival time</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">210</td>
+                    <td class="num">212</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  medSurv_dat &lt;- medSurv_makeup(kmobj_dat, legend = "Before matching", time_scale = time_scale)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">211</td>
+                    <td class="num">213</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  medSurv_dat_adj &lt;- medSurv_makeup(kmobj_dat_adj, legend = "After matching", time_scale = time_scale)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">212</td>
+                    <td class="num">214</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  medSurv_out &lt;- rbind(medSurv_dat, medSurv_dat_adj)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">213</td>
+                    <td class="num">215</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">214</td>
+                    <td class="num">216</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res$inferential[["report_median_surv"]] &lt;- medSurv_out</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">215</td>
+                    <td class="num">217</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">216</td>
+                    <td class="num">218</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # ~~~ Analysis table (Cox model) before and after matching</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">217</td>
+                    <td class="num">219</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : fit PH Cox regression model</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">218</td>
+                    <td class="num">220</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  coxobj_dat &lt;- coxph(Surv(TIME, EVENT) ~ ARM, dat)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">219</td>
+                    <td class="num">221</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  coxobj_dat_adj &lt;- coxph(Surv(TIME, EVENT) ~ ARM, dat, weights = weights, robust = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">220</td>
+                    <td class="num">222</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">221</td>
+                    <td class="num">223</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res$inferential[["coxph_before"]] &lt;- coxobj_dat</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">222</td>
+                    <td class="num">224</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res$inferential[["coxph_after"]] &lt;- coxobj_dat_adj</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">223</td>
+                    <td class="num">225</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">224</td>
+                    <td class="num">226</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : derive ipd exp arm vs agd exp arm</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">225</td>
+                    <td class="num">227</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res_AB$est &lt;- summary(coxobj_dat_adj)$conf.int[1]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">226</td>
+                    <td class="num">228</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  mu &lt;- summary(coxobj_dat_adj)$coef[1]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">227</td>
+                    <td class="num">229</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  sig &lt;- summary(coxobj_dat_adj)$coef[4]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">228</td>
+                    <td class="num">230</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res_AB$se &lt;- sqrt((exp(sig^2) - 1) * exp(2 * mu + sig^2)) # log normal parametrization</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">229</td>
+                    <td class="num">231</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res_AB$ci_l &lt;- summary(coxobj_dat_adj)$conf.int[3]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">230</td>
+                    <td class="num">232</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res_AB$ci_u &lt;- summary(coxobj_dat_adj)$conf.int[4]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">231</td>
+                    <td class="num">233</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res_AB$pval &lt;- summary(coxobj_dat_adj)$coef[6]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">232</td>
+                    <td class="num">234</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">233</td>
+                    <td class="num">235</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : get bootstrapped estimates if applicable</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">234</td>
+                    <td class="num">236</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!is.null(weights_object$boot)) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">235</td>
+                    <td class="num">237</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    keep_rows &lt;- setdiff(seq_len(nrow(weights_object$data)), weights_object$rows_with_missing)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">236</td>
+                    <td class="num">238</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_ipd_id &lt;- weights_object$data[keep_rows, "USUBJID", drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">237</td>
+                    <td class="num">239</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">238</td>
+                    <td class="num">240</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_ipd &lt;- merge(boot_ipd_id, ipd, by = "USUBJID", all.x = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">239</td>
+                    <td class="num">241</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    if (nrow(boot_ipd) != nrow(boot_ipd_id)) stop("ipd has multiple observations for some patients")</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">240</td>
+                    <td class="num">242</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_ipd &lt;- boot_ipd[match(boot_ipd$USUBJID, boot_ipd_id$USUBJID), ]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">241</td>
+                    <td class="num">243</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">242</td>
+                    <td class="num">244</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    stat_fun &lt;- function(data, index, w_obj, pseudo_ipd) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">243</td>
+                    <td class="num">245</td>
                     <td class="coverage">501<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      boot_ipd &lt;- data[index, ]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">244</td>
+                    <td class="num">246</td>
                     <td class="coverage">501<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      r &lt;- dynGet("r", ifnotfound = NA) # Get bootstrap iteration</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">245</td>
+                    <td class="num">247</td>
                     <td class="coverage">501<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      if (!is.na(r)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">246</td>
+                    <td class="num">248</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        if (!all(index == w_obj$boot[, 1, r])) stop("Bootstrap and weight indices don't match")</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">247</td>
+                    <td class="num">249</td>
                     <td class="coverage">500<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        boot_ipd$weights &lt;- w_obj$boot[, 2, r]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">248</td>
+                    <td class="num">250</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">249</td>
+                    <td class="num">251</td>
                     <td class="coverage">501<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      boot_dat &lt;- rbind(boot_ipd, pseudo_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">250</td>
+                    <td class="num">252</td>
                     <td class="coverage">501<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      boot_dat$ARM &lt;- factor(boot_dat$ARM, levels = c(trt_agd, trt_ipd))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">251</td>
+                    <td class="num">253</td>
                     <td class="coverage">501<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      boot_coxobj_dat_adj &lt;- coxph(Surv(TIME, EVENT) ~ ARM, boot_dat, weights = weights)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">252</td>
+                    <td class="num">254</td>
                     <td class="coverage">501<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      c(est = coef(boot_coxobj_dat_adj)[1], var = vcov(boot_coxobj_dat_adj)[1, 1])</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">253</td>
+                    <td class="num">255</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">254</td>
+                    <td class="num">256</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">255</td>
+                    <td class="num">257</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    # Revert seed to how it was for weight bootstrap sampling</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">256</td>
+                    <td class="num">258</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    old_seed &lt;- globalenv()$.Random.seed</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">257</td>
+                    <td class="num">259</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    on.exit(suspendInterrupts(set_random_seed(old_seed)))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">258</td>
+                    <td class="num">260</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    set_random_seed(weights_object$boot_seed)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">259</td>
+                    <td class="num">261</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    R &lt;- dim(weights_object$boot)[3]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">260</td>
+                    <td class="num">262</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">261</td>
+                    <td class="num">263</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_res &lt;- boot(boot_ipd, stat_fun, R = R, w_obj = weights_object, pseudo_ipd = pseudo_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">262</td>
+                    <td class="num">264</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_ci &lt;- boot.ci(boot_res, type = boot_ci_type, w_obj = weights_object, pseudo_ipd = pseudo_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">263</td>
+                    <td class="num">265</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">264</td>
+                    <td class="num">266</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    l_u_index &lt;- switch(boot_ci_type,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">265</td>
+                    <td class="num">267</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "norm" = list(2, 3, "normal"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">266</td>
+                    <td class="num">268</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "basic" = list(4, 5, "basic"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">267</td>
+                    <td class="num">269</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "stud" = list(4, 5, "student"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">268</td>
+                    <td class="num">270</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "perc" = list(4, 5, "percent"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">269</td>
+                    <td class="num">271</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "bca" = list(4, 5, "bca")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">270</td>
+                    <td class="num">272</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">271</td>
+                    <td class="num">273</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">272</td>
+                    <td class="num">274</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    res$inferential[["boot_est"]] &lt;- boot_res</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">273</td>
+                    <td class="num">275</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    transform_estimate &lt;- exp</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">274</td>
+                    <td class="num">276</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_res_AB &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">275</td>
+                    <td class="num">277</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      est = transform_estimate(boot_res$t0[1]),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">276</td>
+                    <td class="num">278</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      se = NA,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">277</td>
+                    <td class="num">279</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      ci_l = transform_estimate(boot_ci[[l_u_index[[3]]]][l_u_index[[1]]]),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">278</td>
+                    <td class="num">280</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      ci_u = transform_estimate(boot_ci[[l_u_index[[3]]]][l_u_index[[2]]]),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">279</td>
+                    <td class="num">281</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      pval = NA</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">280</td>
+                    <td class="num">282</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">281</td>
+                    <td class="num">283</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">282</td>
+                    <td class="num">284</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    res$inferential[["boot_est"]] &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">283</td>
+                    <td class="num">285</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">284</td>
+                    <td class="num">286</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">285</td>
+                    <td class="num">287</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : make analysis report table</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">286</td>
+                    <td class="num">288</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res$inferential[["report_overall_robustCI"]] &lt;- rbind(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">287</td>
+                    <td class="num">289</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    report_table_tte(coxobj_dat, medSurv_dat, tag = paste0("Before matching/", endpoint_name)),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">288</td>
+                    <td class="num">290</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    report_table_tte(coxobj_dat_adj, medSurv_dat_adj, tag = paste0("After matching/", endpoint_name))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">289</td>
+                    <td class="num">291</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">290</td>
+                    <td class="num">292</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">291</td>
+                    <td class="num">293</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (is.null(res$inferential[["boot_est"]])) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">292</td>
+                    <td class="num">294</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    res$inferential[["report_overall_bootCI"]] &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">293</td>
+                    <td class="num">295</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">294</td>
+                    <td class="num">296</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    report_boot &lt;- report_table_tte(coxobj_dat_adj, medSurv_dat_adj, tag = paste0("After matching/", endpoint_name))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">295</td>
+                    <td class="num">297</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    report_boot$`p-Value` &lt;- NA</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">296</td>
+                    <td class="num">298</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    report_boot$`HR[95% CI]`[1] &lt;- do.call(sprintf, args = c(list(fmt = "%.2f[%.2f;%.2f]"), boot_res_AB[1:3]))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">297</td>
+                    <td class="num">299</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    res$inferential[["report_overall_bootCI"]] &lt;- rbind(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">298</td>
+                    <td class="num">300</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      report_table_tte(coxobj_dat, medSurv_dat, tag = paste0("Before matching/", endpoint_name)),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">299</td>
+                    <td class="num">301</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      report_boot</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">300</td>
+                    <td class="num">302</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">301</td>
+                    <td class="num">303</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">302</td>
+                    <td class="num">304</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">303</td>
+                    <td class="num">305</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # output</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">304</td>
+                    <td class="num">306</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">305</td>
+                    <td class="num">307</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">306</td>
+                    <td class="num">308</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">307</td>
+                    <td class="num">309</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"># MAIC inference functions for Binary outcome type ------------</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">308</td>
+                    <td class="num">310</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">309</td>
+                    <td class="num">311</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">maic_unanchored_binary &lt;- function(res,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">310</td>
+                    <td class="num">312</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   res_AB,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">311</td>
+                    <td class="num">313</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   dat,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">312</td>
+                    <td class="num">314</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">313</td>
+                    <td class="num">315</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   pseudo_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">314</td>
+                    <td class="num">316</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   binary_robust_cov_type,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">315</td>
+                    <td class="num">317</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   weights_object,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">316</td>
+                    <td class="num">318</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   endpoint_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">317</td>
+                    <td class="num">319</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   eff_measure,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">318</td>
+                    <td class="num">320</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   boot_ci_type,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">319</td>
+                    <td class="num">321</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   trt_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">320</td>
+                    <td class="num">322</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">                                   trt_agd) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">321</td>
+                    <td class="num">323</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # ~~~ Analysis table</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">322</td>
+                    <td class="num">324</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : set up proper link</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">323</td>
+                    <td class="num">325</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  glm_link &lt;- switch(eff_measure,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">324</td>
+                    <td class="num">326</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    "RD" = poisson(link = "identity"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">325</td>
+                    <td class="num">327</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    "RR" = poisson(link = "log"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">326</td>
+                    <td class="num">328</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    "OR" = binomial(link = "logit")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">327</td>
+                    <td class="num">329</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">328</td>
+                    <td class="num">330</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  transform_estimate &lt;- switch(eff_measure,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">329</td>
+                    <td class="num">331</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    "RD" = function(x) x * 100,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">330</td>
+                    <td class="num">332</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    "RR" = exp,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">331</td>
+                    <td class="num">333</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    "OR" = exp</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">332</td>
+                    <td class="num">334</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">333</td>
+                    <td class="num">335</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">334</td>
+                    <td class="num">336</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : fit glm for binary outcome and robust estimate with weights</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">335</td>
+                    <td class="num">337</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  binobj_dat &lt;- glm(RESPONSE ~ ARM, dat, family = glm_link)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">336</td>
+                    <td class="num">338</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  binobj_dat_adj &lt;- glm(RESPONSE ~ ARM, dat, weights = weights, family = glm_link)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">337</td>
+                    <td class="num">339</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  bin_robust_cov &lt;- sandwich::vcovHC(binobj_dat_adj, type = binary_robust_cov_type)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">338</td>
+                    <td class="num">340</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  bin_robust_coef &lt;- lmtest::coeftest(binobj_dat_adj, vcov. = bin_robust_cov)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">339</td>
+                    <td class="num">341</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  bin_robust_ci &lt;- lmtest::coefci(binobj_dat_adj, vcov. = bin_robust_cov)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">340</td>
+                    <td class="num">342</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">341</td>
+                    <td class="num">343</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res$inferential[["model_before"]] &lt;- binobj_dat</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">342</td>
+                    <td class="num">344</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res$inferential[["model_after"]] &lt;- binobj_dat_adj</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">343</td>
+                    <td class="num">345</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">344</td>
+                    <td class="num">346</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res_AB$est &lt;- transform_estimate(bin_robust_coef[2, "Estimate"])</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">345</td>
+                    <td class="num">347</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res_AB$ci_l &lt;- transform_estimate(bin_robust_ci[2, "2.5 %"])</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">346</td>
+                    <td class="num">348</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res_AB$ci_u &lt;- transform_estimate(bin_robust_ci[2, "97.5 %"])</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">347</td>
+                    <td class="num">349</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res_AB$pval &lt;- bin_robust_coef[2, "Pr(&gt;|z|)"]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">348</td>
+                    <td class="num">350</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">349</td>
+                    <td class="num">351</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : get bootstrapped estimates if applicable</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">350</td>
+                    <td class="num">352</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!is.null(weights_object$boot)) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">351</td>
+                    <td class="num">353</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    keep_rows &lt;- setdiff(seq_len(nrow(weights_object$data)), weights_object$rows_with_missing)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">352</td>
+                    <td class="num">354</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_ipd_id &lt;- weights_object$data[keep_rows, "USUBJID", drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">353</td>
+                    <td class="num">355</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">354</td>
+                    <td class="num">356</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_ipd &lt;- merge(boot_ipd_id, ipd, by = "USUBJID", all.x = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">355</td>
+                    <td class="num">357</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    if (nrow(boot_ipd) != nrow(boot_ipd_id)) stop("ipd has multiple observations for some patients")</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">356</td>
+                    <td class="num">358</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_ipd &lt;- boot_ipd[match(boot_ipd$USUBJID, boot_ipd_id$USUBJID), ]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">357</td>
+                    <td class="num">359</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">358</td>
+                    <td class="num">360</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    stat_fun &lt;- function(data, index, w_obj, pseudo_ipd) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">359</td>
+                    <td class="num">361</td>
                     <td class="coverage">21<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      boot_ipd &lt;- data[index, ]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">360</td>
+                    <td class="num">362</td>
                     <td class="coverage">21<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      r &lt;- dynGet("r", ifnotfound = NA) # Get bootstrap iteration</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">361</td>
+                    <td class="num">363</td>
                     <td class="coverage">21<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      if (!is.na(r)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">362</td>
+                    <td class="num">364</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        if (!all(index == w_obj$boot[, 1, r])) stop("Bootstrap and weight indices don't match")</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">363</td>
+                    <td class="num">365</td>
                     <td class="coverage">20<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        boot_ipd$weights &lt;- w_obj$boot[, 2, r]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">364</td>
+                    <td class="num">366</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">365</td>
+                    <td class="num">367</td>
                     <td class="coverage">21<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      boot_dat &lt;- rbind(boot_ipd, pseudo_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">366</td>
+                    <td class="num">368</td>
                     <td class="coverage">21<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      boot_dat$ARM &lt;- factor(boot_dat$ARM, levels = c(trt_agd, trt_ipd))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">367</td>
+                    <td class="num">369</td>
                     <td class="coverage">21<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      boot_binobj_dat_adj &lt;- glm(RESPONSE ~ ARM, boot_dat, weights = weights, family = glm_link)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">368</td>
+                    <td class="num">370</td>
                     <td class="coverage">21<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      c(est = coef(boot_binobj_dat_adj)[2], var = vcov(boot_binobj_dat_adj)[2, 2])</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">369</td>
+                    <td class="num">371</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">370</td>
+                    <td class="num">372</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">371</td>
+                    <td class="num">373</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    # Revert seed to how it was for weight bootstrap sampling</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">372</td>
+                    <td class="num">374</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    old_seed &lt;- globalenv()$.Random.seed</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">373</td>
+                    <td class="num">375</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    on.exit(suspendInterrupts(set_random_seed(old_seed)))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">374</td>
+                    <td class="num">376</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    set_random_seed(weights_object$boot_seed)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">375</td>
+                    <td class="num">377</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    R &lt;- dim(weights_object$boot)[3]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">376</td>
+                    <td class="num">378</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_res &lt;- boot(boot_ipd, stat_fun, R = R, w_obj = weights_object, pseudo_ipd = pseudo_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">377</td>
+                    <td class="num">379</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_ci &lt;- boot.ci(boot_res, type = boot_ci_type, w_obj = weights_object, pseudo_ipd = pseudo_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">378</td>
+                    <td class="num">380</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">379</td>
+                    <td class="num">381</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    l_u_index &lt;- switch(boot_ci_type,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">380</td>
+                    <td class="num">382</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "norm" = list(2, 3, "normal"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">381</td>
+                    <td class="num">383</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "basic" = list(4, 5, "basic"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">382</td>
+                    <td class="num">384</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "stud" = list(4, 5, "student"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">383</td>
+                    <td class="num">385</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "perc" = list(4, 5, "percent"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">384</td>
+                    <td class="num">386</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      "bca" = list(4, 5, "bca")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">385</td>
+                    <td class="num">387</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">386</td>
+                    <td class="num">388</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">387</td>
+                    <td class="num">389</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    res$inferential[["boot_est"]] &lt;- boot_res</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">388</td>
+                    <td class="num">390</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    boot_res_AB &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">389</td>
+                    <td class="num">391</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      est = transform_estimate(boot_res$t0[1]),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">390</td>
+                    <td class="num">392</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      ci_l = transform_estimate(boot_ci[[l_u_index[[3]]]][l_u_index[[1]]]),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">391</td>
+                    <td class="num">393</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      ci_u = transform_estimate(boot_ci[[l_u_index[[3]]]][l_u_index[[2]]]),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">392</td>
+                    <td class="num">394</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      pval = NA</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">393</td>
+                    <td class="num">395</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">394</td>
+                    <td class="num">396</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">395</td>
+                    <td class="num">397</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    res$inferential[["boot_est"]] &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">396</td>
+                    <td class="num">398</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">397</td>
+                    <td class="num">399</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">398</td>
+                    <td class="num">400</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  # : make analysis report table</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">399</td>
+                    <td class="num">401</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res$inferential[["report_overall_robustCI"]] &lt;- rbind(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">400</td>
+                    <td class="num">402</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    report_table_binary(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">401</td>
+                    <td class="num">403</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      binobj_dat,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">402</td>
+                    <td class="num">404</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      tag = paste0("Before matching/", endpoint_name),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">403</td>
+                    <td class="num">405</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      eff_measure = eff_measure</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">404</td>
+                    <td class="num">406</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">405</td>
+                    <td class="num">407</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    report_table_binary(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">406</td>
+                    <td class="num">408</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      binobj_dat_adj,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">407</td>
+                    <td class="num">409</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      res_AB,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">408</td>
+                    <td class="num">410</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      tag = paste0("After matching/", endpoint_name),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">409</td>
+                    <td class="num">411</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      eff_measure = eff_measure</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">410</td>
+                    <td class="num">412</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">411</td>
+                    <td class="num">413</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">412</td>
+                    <td class="num">414</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (is.null(res$inferential[["boot_est"]])) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">413</td>
+                    <td class="num">415</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    res$inferential[["report_overall_bootCI"]] &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">414</td>
+                    <td class="num">416</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">415</td>
+                    <td class="num">417</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    res$inferential[["report_overall_bootCI"]] &lt;- rbind(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">416</td>
+                    <td class="num">418</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      report_table_binary(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">417</td>
+                    <td class="num">419</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        binobj_dat,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">418</td>
+                    <td class="num">420</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        tag = paste0("Before matching/", endpoint_name),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">419</td>
+                    <td class="num">421</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        eff_measure = eff_measure</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">420</td>
+                    <td class="num">422</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">421</td>
+                    <td class="num">423</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      report_table_binary(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">422</td>
+                    <td class="num">424</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        binobj_dat_adj,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">423</td>
+                    <td class="num">425</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        boot_res_AB,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">424</td>
+                    <td class="num">426</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        tag = paste0("After matching/", endpoint_name),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">425</td>
+                    <td class="num">427</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        eff_measure = eff_measure</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">426</td>
+                    <td class="num">428</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">427</td>
+                    <td class="num">429</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">428</td>
+                    <td class="num">430</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">429</td>
+                    <td class="num">431</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  res</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">430</td>
+                    <td class="num">432</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
@@ -12888,147 +12729,147 @@ <h2>maicplus coverage - 54.75%</h2>
                 </tbody>
               </table>
             </div>
-            <div id="R/matching.R" class="hidden">
+            <div id="R/plot_km.R" class="hidden">
               <table class="table-condensed">
                 <tbody>
                   <tr class="never">
                     <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># Functions for matching step: estimation of individual weights</pre>
+                      <pre class="language-r">#' Kaplan Meier (KM) plot function for anchored and unanchored cases</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># functions to be exported ---------------------------------------</pre>
+                      <pre class="language-r">#' It is wrapper function of \code{basic_kmplot}. The argument setting is similar to \code{maic_anchored} and</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' \code{maic_unanchored}, and it is used in those two functions.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Derive individual weights in the matching step of MAIC</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @param weights_object an object returned by \code{estimate_weight}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Assuming data is properly processed, this function takes individual patient data (IPD) with centered covariates</pre>
+                      <pre class="language-r">#' @param tte_ipd a data frame of individual patient data (IPD) of internal trial, contain at least `"USUBJID"`,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' (effect modifiers and/or prognostic variables) as input, and generates weights for each individual in IPD trial to</pre>
+                      <pre class="language-r">#'   `"EVENT"`, `"TIME"` columns and a column indicating treatment assignment</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' match the covariates in aggregate data.</pre>
+                      <pre class="language-r">#' @param tte_pseudo_ipd a data frame of pseudo IPD by digitized KM curves of external trial (for time-to-event</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   endpoint), contain at least `"EVENT"`, `"TIME"`</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param data a numeric matrix, centered covariates of IPD, no missing value in any cell is allowed</pre>
+                      <pre class="language-r">#' @param trt_ipd  a string, name of the interested investigation arm in internal trial \code{dat_igd} (real IPD)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param centered_colnames a character or numeric vector (column indicators) of centered covariates</pre>
+                      <pre class="language-r">#' @param trt_agd a string, name of the interested investigation arm in external trial \code{dat_pseudo} (pseudo IPD)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param start_val a scalar, the starting value for all coefficients of the propensity score regression</pre>
+                      <pre class="language-r">#' @param trt_common a string, name of the common comparator in internal and external trial, by default is NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param method a string, name of the optimization algorithm (see 'method' argument of \code{base::optim()}) The</pre>
+                      <pre class="language-r">#'   indicating unanchored case</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   default is `"BFGS"`, other options are `"Nelder-Mead"`, `"CG"`, `"L-BFGS-B"`, `"SANN"`, and `"Brent"`</pre>
+                      <pre class="language-r">#' @param trt_var_ipd a string, column name in \code{tte_ipd} that contains the treatment assignment</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param n_boot_iteration an integer, number of bootstrap iterations. By default is NULL which means bootstrapping</pre>
+                      <pre class="language-r">#' @param trt_var_agd a string, column name in \code{tte_pseudo_ipd} that contains the treatment assignment</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   procedure will not be triggered, and hence the element `"boot"` of output list object will be NULL.</pre>
+                      <pre class="language-r">#' @param km_conf_type a string, pass to \code{conf.type} of \code{survfit}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param set_seed_boot a scalar, the random seed for conducting the bootstrapping, only relevant if</pre>
+                      <pre class="language-r">#' @param km_layout a string, only applicable for unanchored case (\code{trt_common = NULL}), indicated the desired</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \code{n_boot_iteration} is not NULL. By default, use seed 1234</pre>
+                      <pre class="language-r">#'   layout of output KM curve.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ... Additional `control` parameters passed to [stats::optim].</pre>
+                      <pre class="language-r">#' @param ... other arguments in \code{basic_kmplot}</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -13042,1379 +12883,1379 @@ <h2>maicplus coverage - 54.75%</h2>
                     <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a list with the following 4 elements,</pre>
+                      <pre class="language-r">#' @return In unanchored case, a KM plot with risk set table. In anchored case, depending on \code{km_layout},</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' \describe{</pre>
+                      <pre class="language-r">#' \itemize{</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{data}{a data.frame, includes the input \code{data} with appended column 'weights' and 'scaled_weights'.</pre>
+                      <pre class="language-r">#'   \item if "by_trial", 2 by 1 plot, first all KM curves (incl. weighted) in IPD trial, and then KM curves in AgD</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   Scaled weights has a summation to be the number of rows in \code{data} that has no missing value in any of the</pre>
+                      <pre class="language-r">#'   trial, with risk set table.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   effect modifiers}</pre>
+                      <pre class="language-r">#'   \item if "by_arm", 2 by 1 plot, first KM curves of \code{trt_agd} and  \code{trt_ipd} (with and without weights),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{centered_colnames}{column names of centered effect modifiers in \code{data}}</pre>
+                      <pre class="language-r">#'    and then KM curves of \code{trt_common} in AgD trial and IPD trial (with and without weights). Risk set table is</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{nr_missing}{number of rows in \code{data} that has at least 1 missing value in specified centered effect</pre>
+                      <pre class="language-r">#'     appended.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   modifiers}</pre>
+                      <pre class="language-r">#'   \item if "all", 2 by 2 plot, all plots in "by_trial" and "by_arm" without risk set table appended.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{ess}{effective sample size, square of sum divided by sum of squares}</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{opt}{R object returned by \code{base::optim()}, for assess convergence and other details}</pre>
+                      <pre class="language-r">#' @example inst/examples/kmplot_anchored_ex.R</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item{boot}{a n by 2 by k array or NA, where n equals to number of rows in \code{data}, and k equals</pre>
+                      <pre class="language-r">#' @example inst/examples/kmplot_unanchored_ex.R</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'      \code{n_boot_iteration}. The 2 columns in the second dimension include a column of numeric indexes of the rows</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'      in \code{data} that are selected at a bootstrapping iteration and a column of weights. \code{boot} is NA when</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'      argument \code{n_boot_iteration} is set as NULL</pre>
+                      <pre class="language-r">kmplot &lt;- function(weights_object,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   }</pre>
+                      <pre class="language-r">                   tte_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">                   tte_pseudo_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                   trt_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">                   trt_agd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data(agd)</pre>
+                      <pre class="language-r">                   trt_common = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data(adsl_sat)</pre>
+                      <pre class="language-r">                   trt_var_ipd = "ARM",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">42</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ipd_centered &lt;- center_ipd(ipd = adsl_sat, agd = process_agd(agd))</pre>
+                      <pre class="language-r">                   trt_var_agd = "ARM",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">43</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' centered_colnames &lt;- grep("_CENTERED", colnames(ipd_centered), value = TRUE)</pre>
+                      <pre class="language-r">                   km_conf_type = "log-log",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">44</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' centered_colnames</pre>
+                      <pre class="language-r">                   km_layout = c("all", "by_trial", "by_arm"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">45</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' weighted_data &lt;- estimate_weights(data = ipd_centered, centered_colnames = centered_colnames)</pre>
+                      <pre class="language-r">                   ...) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">46</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' \donttest{</pre>
+                      <pre class="language-r">  names(tte_ipd) &lt;- toupper(names(tte_ipd))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">47</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # To later estimate bootstrap confidence intervals, we calculate the weights</pre>
+                      <pre class="language-r">  names(tte_pseudo_ipd) &lt;- toupper(names(tte_pseudo_ipd))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">48</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # for the bootstrap samples:</pre>
+                      <pre class="language-r">  trt_var_ipd &lt;- toupper(trt_var_ipd)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">49</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' weighted_data_boot &lt;- estimate_weights(</pre>
+                      <pre class="language-r">  trt_var_agd &lt;- toupper(trt_var_agd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">50</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data = ipd_centered, centered_colnames = centered_colnames, n_boot_iteration = 500</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">51</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">52</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">  on.exit(par(original_par))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">53</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # pre check</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">55</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">estimate_weights &lt;- function(data,</pre>
+                      <pre class="language-r">  if (!"maicplus_estimate_weights" %in% class(weights_object)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">56</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             centered_colnames = NULL,</pre>
+                      <pre class="language-r">    stop("weights_object should be an object returned by estimate_weights")</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">57</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             start_val = 0,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">58</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             method = "BFGS",</pre>
+                      <pre class="language-r">  if (!all(c("USUBJID", "TIME", "EVENT", trt_var_ipd) %in% names(tte_ipd))) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">59</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             n_boot_iteration = NULL,</pre>
+                      <pre class="language-r">    stop("tte_ipd needs to include at least USUBJID, TIME, EVENT, ", trt_var_ipd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             set_seed_boot = 1234,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">61</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             ...) {</pre>
+                      <pre class="language-r">  if (!all(c("TIME", "EVENT", trt_var_agd) %in% names(tte_pseudo_ipd))) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">62</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # pre check</pre>
+                      <pre class="language-r">    stop("tte_pseudo_ipd needs to include at least TIME, EVENT, ", trt_var_agd)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">63</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ch1 &lt;- is.data.frame(data)</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">64</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!ch1) {</pre>
+                      <pre class="language-r">  km_layout &lt;- match.arg(km_layout, choices = c("all", "by_trial", "by_arm"), several.ok = FALSE)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">65</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("'data' is not a data.frame")</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">66</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  # preparing data</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">67</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  is_anchored &lt;- !is.null(trt_common)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">68</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ch2 &lt;- (!is.null(centered_colnames))</pre>
+                      <pre class="language-r">  tte_ipd &lt;- tte_ipd[tte_ipd[[trt_var_ipd]] %in% c(trt_ipd, trt_common), , drop = FALSE]</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">69</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (ch2 &amp;&amp; is.numeric(centered_colnames)) {</pre>
+                      <pre class="language-r">  tte_pseudo_ipd &lt;- tte_pseudo_ipd[tte_pseudo_ipd[[trt_var_agd]] %in% c(trt_agd, trt_common), , drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">70</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ch2b &lt;- any(centered_colnames &lt; 1 | centered_colnames &gt; ncol(data))</pre>
+                      <pre class="language-r">  tte_ipd$weights &lt;- weights_object$data$weights[match(weights_object$data$USUBJID, tte_ipd$USUBJID)]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">71</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (ch2b) {</pre>
+                      <pre class="language-r">  tte_pseudo_ipd$weights &lt;- 1</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">72</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("specified centered_colnames are out of bound")</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">73</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">  # generate plot</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">74</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else if (ch2 &amp;&amp; is.character(centered_colnames)) {</pre>
+                      <pre class="language-r">  if (!is_anchored) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">75</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ch2b &lt;- !all(centered_colnames %in% names(data))</pre>
+                      <pre class="language-r">    ## unanchored case</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">76</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (ch2b) {</pre>
+                      <pre class="language-r">    kmobj_B &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_agd)),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">77</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("1 or more specified centered_colnames are not found in 'data'")</pre>
+                      <pre class="language-r">      data = tte_pseudo_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">78</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">      conf.type = km_conf_type</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">79</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">80</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("'centered_colnames' should be either a numeric or character vector")</pre>
+                      <pre class="language-r">    kmobj_A &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">81</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">      data = tte_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">82</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      conf.type = km_conf_type</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">83</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ch3 &lt;- sapply(centered_colnames, function(ii) {</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">84</td>
-                    <td class="coverage">66<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    !is.numeric(data[[ii]])</pre>
+                      <pre class="language-r">    kmobj_A_adj &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">85</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">      data = tte_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">86</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (any(ch3)) {</pre>
+                      <pre class="language-r">      conf.type = km_conf_type,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">87</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop(paste0(</pre>
+                      <pre class="language-r">      weights = weights</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">88</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "following columns of 'data' are not numeric for the calculation:",</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">89</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      paste(which(ch3), collapse = ",")</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">90</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ))</pre>
+                      <pre class="language-r">    kmdat &lt;- do.call(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">91</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">      rbind,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">92</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      c(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">93</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # prepare data for optimization</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_B, trt_agd),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">94</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(centered_colnames)) centered_colnames &lt;- seq_len(ncol(data))</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_A, trt_ipd),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">95</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  EM &lt;- data[, centered_colnames, drop = FALSE]</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_A_adj, paste(trt_ipd, "(weighted)"))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">96</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ind &lt;- apply(EM, 1, function(xx) any(is.na(xx)))</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">97</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  nr_missing &lt;- sum(ind)</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">98</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  rows_with_missing &lt;- which(ind)</pre>
+                      <pre class="language-r">    kmdat$treatment &lt;- factor(kmdat$treatment, levels = unique(kmdat$treatment))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">99</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  EM &lt;- as.matrix(EM[!ind, , drop = FALSE])</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">100</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    basic_kmplot(kmdat,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">101</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # estimate weights</pre>
+                      <pre class="language-r">      show_risk_set = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">102</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  opt1 &lt;- optimise_weights(matrix = EM, par = rep(start_val, ncol(EM)), method = method, ...)</pre>
+                      <pre class="language-r">      main_title = "Kaplan-Meier Curves",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">103</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  alpha &lt;- opt1$alpha</pre>
+                      <pre class="language-r">      subplot_heights = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">104</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt &lt;- opt1$wt</pre>
+                      <pre class="language-r">      suppress_plot_layout = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">105</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt_rs &lt;- (wt / sum(wt)) * nrow(EM)</pre>
+                      <pre class="language-r">      ...</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">106</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">107</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # bootstrapping</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">108</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  outboot &lt;- if (is.null(n_boot_iteration)) {</pre>
+                      <pre class="language-r">    # anchored case</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">109</td>
-                    <td class="coverage">7<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_seed &lt;- NULL</pre>
+                      <pre class="language-r">    # - agd trial km data</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">110</td>
-                    <td class="coverage">7<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_strata &lt;- NULL</pre>
+                      <pre class="language-r">    kmobj_C_S1 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_agd)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">111</td>
-                    <td class="coverage">7<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    NULL</pre>
+                      <pre class="language-r">      data = tte_pseudo_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">112</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">      conf.type = km_conf_type,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">113</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Make sure to leave '.Random.seed' as-is on exit</pre>
+                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_pseudo_ipd$", trt_var_agd, " == '", trt_common, "')")))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">114</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    old_seed &lt;- globalenv()$.Random.seed</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">115</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    on.exit(suspendInterrupts(set_random_seed(old_seed)))</pre>
+                      <pre class="language-r">    kmobj_B_S1 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_agd)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">116</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    set.seed(set_seed_boot)</pre>
+                      <pre class="language-r">      data = tte_pseudo_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">117</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      conf.type = km_conf_type,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">118</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    rowid_in_data &lt;- which(!ind)</pre>
+                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_pseudo_ipd$", trt_var_agd, " == '", trt_agd, "')")))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">119</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    arms &lt;- factor(data$ARM[rowid_in_data])</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">120</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_statistic &lt;- function(d, w) optimise_weights(d[w, ], par = alpha, method = method, ...)$wt[, 1]</pre>
+                      <pre class="language-r">    # - ipd trial km data</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">121</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_out &lt;- boot(EM, statistic = boot_statistic, R = n_boot_iteration, strata = arms)</pre>
+                      <pre class="language-r">    kmobj_C_S2 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">122</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      data = tte_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">123</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_array &lt;- array(dim = list(nrow(EM), 2, n_boot_iteration))</pre>
+                      <pre class="language-r">      conf.type = km_conf_type,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">124</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    dimnames(boot_array) &lt;- list(sampled_patient = NULL, c("rowid", "weight"), bootstrap_iteration = NULL)</pre>
+                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_ipd$", trt_var_ipd, " == '", trt_common, "')")))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">125</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_array[, 1, ] &lt;- t(boot.array(boot_out, TRUE))</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">126</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_array[, 2, ] &lt;- t(boot_out$t)</pre>
+                      <pre class="language-r">    kmobj_A_S2 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">127</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_seed &lt;- boot_out$seed</pre>
+                      <pre class="language-r">      data = tte_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">128</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_strata &lt;- boot_out$strata</pre>
+                      <pre class="language-r">      conf.type = km_conf_type,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">129</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_array</pre>
+                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_ipd$", trt_var_ipd, " == '", trt_ipd, "')")))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">130</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">131</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    # - ipd trial km data with weights</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">132</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # append weights to data</pre>
+                      <pre class="language-r">    kmobj_Cadj_S2 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">133</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data$weights &lt;- NA</pre>
+                      <pre class="language-r">      data = tte_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">134</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data$weights[!ind] &lt;- wt</pre>
+                      <pre class="language-r">      conf.type = km_conf_type,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">135</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      weights = weights,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">136</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data$scaled_weights &lt;- NA</pre>
+                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_ipd$", trt_var_ipd, " == '", trt_common, "')")))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">137</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data$scaled_weights[!ind] &lt;- wt_rs</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">138</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    kmobj_Aadj_S2 &lt;- survfit(as.formula(paste("Surv(TIME, EVENT) ~", trt_var_ipd)),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">139</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.numeric(centered_colnames)) centered_colnames &lt;- names(data)[centered_colnames]</pre>
+                      <pre class="language-r">      data = tte_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">140</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      conf.type = km_conf_type,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">141</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # Output</pre>
+                      <pre class="language-r">      weights = weights,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">142</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  outdata &lt;- list(</pre>
+                      <pre class="language-r">      subset = eval(parse(text = paste0("(tte_ipd$", trt_var_ipd, " == '", trt_ipd, "')")))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">143</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    data = data,</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">144</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    centered_colnames = centered_colnames,</pre>
+                      <pre class="language-r">    # - plotdat for layout by trial</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">145</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    nr_missing = nr_missing,</pre>
+                      <pre class="language-r">    kmdat_s2 &lt;- do.call(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">146</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ess = sum(wt)^2 / sum(wt^2),</pre>
+                      <pre class="language-r">      rbind,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">147</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    opt = opt1$opt,</pre>
+                      <pre class="language-r">      c(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">148</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot = outboot,</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_C_S2, trt_common),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">149</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_seed = boot_seed,</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_A_S2, trt_ipd),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">150</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_strata = boot_strata,</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_Aadj_S2, paste(trt_ipd, "(weighted)")),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">151</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    rows_with_missing = rows_with_missing</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_Cadj_S2, paste(trt_common, "(weighted)"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">152</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">153</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">154</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  class(outdata) &lt;- c("maicplus_estimate_weights", "list")</pre>
+                      <pre class="language-r">    kmdat_s2$treatment &lt;- factor(kmdat_s2$treatment, levels = unique(kmdat_s2$treatment))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">155</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  outdata</pre>
+                      <pre class="language-r">    kmdat_s1 &lt;- do.call(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">156</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      rbind,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">157</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      c(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">158</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_C_S1, trt_common),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">159</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Estimate weights using `optim`</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_B_S1, trt_agd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">160</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">161</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param matrix Matrix of data to be used for estimating weights</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">162</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param par Vector of starting values for the parameters with length equal to the number of columns in `matrix`</pre>
+                      <pre class="language-r">    kmdat_s1$treatment &lt;- factor(kmdat_s1$treatment, levels = unique(kmdat_s1$treatment))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">163</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param method Method parameter passed to [stats::optim]</pre>
+                      <pre class="language-r">    # - plotdat for layout by arm</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">164</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ... Additional `control` parameters passed to [stats::optim]</pre>
+                      <pre class="language-r">    kmdat_a2 &lt;- do.call(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">165</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      rbind,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">166</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return List containing estimated `alpha` values and `wt` weights for all rows of matrix</pre>
+                      <pre class="language-r">      c(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">167</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @noRd</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_B_S1, trt_agd),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">168</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">optimise_weights &lt;- function(matrix,</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_A_S2, trt_ipd),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">169</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             par = rep(0, ncol(matrix)),</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_Aadj_S2, paste(trt_ipd, "(weighted)"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">170</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             method = "BFGS",</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">171</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             maxit = 300,</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">172</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             trace = 0,</pre>
+                      <pre class="language-r">    kmdat_a2$treatment &lt;- factor(kmdat_a2$treatment, levels = unique(kmdat_a2$treatment))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">173</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             ...) {</pre>
+                      <pre class="language-r">    kmdat_a1 &lt;- do.call(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">174</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!all(is.numeric(par) || is.finite(par), length(par) == ncol(matrix))) {</pre>
+                      <pre class="language-r">      rbind,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">175</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("par must be a numeric vector with finite values of length equal to the number of columns in 'matrix'")</pre>
+                      <pre class="language-r">      c(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">176</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_C_S1, paste(trt_common, "(AgD)")),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">177</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  opt1 &lt;- optim(</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_C_S2, paste(trt_common, "(IPD)")),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">178</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    par = par,</pre>
+                      <pre class="language-r">        survfit_makeup(kmobj_Cadj_S2, paste(trt_common, "(IPD,weighted)"))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">179</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    fn = function(alpha, X) sum(exp(X %*% alpha)),</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">180</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    gr = function(alpha, X) colSums(sweep(X, 1, exp(X %*% alpha), "*")),</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">181</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    X = matrix,</pre>
+                      <pre class="language-r">    kmdat_a1$treatment &lt;- factor(kmdat_a1$treatment, levels = unique(kmdat_a1$treatment))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">182</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    method = method,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">183</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    control = list(maxit = maxit, trace = trace, ...)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">    # make plot depending on the layout</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">185</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (opt1$convergence != 0) {</pre>
+                      <pre class="language-r">    if (km_layout == "by_trial") {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">186</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    warning(</pre>
+                      <pre class="language-r">      # 1 by 2 plot, each plot is per trial</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">187</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "optim() did not converge. ",</pre>
+                      <pre class="language-r">      subplot_heights &lt;- c(7, 0.7 + 2 * 0.7, 0.8)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">188</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      opt1$message,</pre>
+                      <pre class="language-r">      layout_mat &lt;- matrix(1:4, ncol = 2)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">189</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "\nSee ?optim for more information on convergence code: ", opt1$convergence</pre>
+                      <pre class="language-r">      layout(layout_mat, heights = subplot_heights)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">190</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">191</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">      basic_kmplot(kmdat_s2,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">192</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  list(</pre>
+                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_common, ") in the IPD trial"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">193</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    opt = opt1,</pre>
+                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">194</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    alpha = opt1$par,</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">195</td>
-                    <td class="coverage">544<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    wt = exp(matrix %*% opt1$par)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">196</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      basic_kmplot(kmdat_s1,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">197</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_agd, " vs ", trt_common, ") in the AgD trial"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">198</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">199</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Calculate Statistics for Weight Plot Legend</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">200</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    } else if (km_layout == "by_arm") {</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">201</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Calculates ESS reduction and median weights which is used to create legend for weights plot</pre>
+                      <pre class="language-r">      # 1 by 2 plot, by 1 is for investigational arm, the other is for common comparator</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">202</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      subplot_heights &lt;- c(7, 0.7 + 2 * 0.7, 0.8)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">203</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param weighted_data object returned after calculating weights using [estimate_weights]</pre>
+                      <pre class="language-r">      layout_mat &lt;- matrix(1:4, ncol = 2)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">204</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      layout(layout_mat, heights = subplot_heights)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">205</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return list of ESS, ESS reduction, median value of scaled and unscaled weights, and missing count</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">206</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">      basic_kmplot(kmdat_a2,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">207</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data("weighted_sat")</pre>
+                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_agd, ")"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">208</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' calculate_weights_legend(weighted_sat)</pre>
+                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">209</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">210</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @keywords internal</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">211</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      basic_kmplot(kmdat_a1,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">212</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">calculate_weights_legend &lt;- function(weighted_data) {</pre>
+                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves of Common Comparator \n", trt_common, "(IPD vs AgD Trial)"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">213</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!inherits(weighted_data, "maicplus_estimate_weights")) {</pre>
+                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">214</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("weighted_data must be class `maicplus_estimate_weights` generated by estimate_weights()")</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">215</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    } else {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">216</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ess &lt;- weighted_data$ess</pre>
+                      <pre class="language-r">      # 2 by 2 plot, combine by trial and by arm</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">217</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt &lt;- weighted_data$data$weights</pre>
+                      <pre class="language-r">      layout_mat &lt;- matrix(1:4, ncol = 2, byrow = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">218</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt_scaled &lt;- weighted_data$data$scaled_weights</pre>
+                      <pre class="language-r">      layout(layout_mat)</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -14424,39 +14265,39 @@ <h2>maicplus coverage - 54.75%</h2>
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">220</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # calculate sample size and exclude NA from wt</pre>
+                      <pre class="language-r">      basic_kmplot(kmdat_s2,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">221</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  nr_na &lt;- sum(is.na(wt))</pre>
+                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_common, ") in the IPD trial"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">222</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  n &lt;- length(wt) - nr_na</pre>
+                      <pre class="language-r">        show_risk_set = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">223</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt &lt;- na.omit(wt)</pre>
+                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">224</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt_scaled &lt;- na.omit(wt_scaled)</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -14466,165 +14307,165 @@ <h2>maicplus coverage - 54.75%</h2>
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">226</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # calculate ess reduction and median weights</pre>
+                      <pre class="language-r">      basic_kmplot(kmdat_s1,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">227</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ess_reduction &lt;- (1 - (ess / n)) * 100</pre>
+                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_agd, " vs ", trt_common, ") in the AgD trial"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">228</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt_median &lt;- median(wt)</pre>
+                      <pre class="language-r">        show_risk_set = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">229</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt_scaled_median &lt;- median(wt_scaled)</pre>
+                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">230</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">231</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  list(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">232</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ess = round(ess, 2),</pre>
+                      <pre class="language-r">      basic_kmplot(kmdat_a2,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">233</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ess_reduction = round(ess_reduction, 2),</pre>
+                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_agd, ")"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">234</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    wt_median = round(wt_median, 4),</pre>
+                      <pre class="language-r">        show_risk_set = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">235</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    wt_scaled_median = round(wt_scaled_median, 4),</pre>
+                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">236</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    nr_na = nr_na</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">237</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">238</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      basic_kmplot(kmdat_a1,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">239</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        main_title = paste0("Kaplan-Meier Curves of Common Comparator \n", trt_common, "(IPD vs AgD Trial)"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">240</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Plot MAIC weights in a histogram with key statistics in legend</pre>
+                      <pre class="language-r">        show_risk_set = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">241</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        suppress_plot_layout = TRUE, ...</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">242</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Generates a base R histogram of weights. Default is to plot either unscaled or scaled weights and not both.</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">243</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">244</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param weighted_data object returned after calculating weights using [estimate_weights]</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">245</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param bin_col a string, color for the bins of histogram</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">246</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param vline_col a string, color for the vertical line in the histogram</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">247</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param main_title title of the plot</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">248</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param scaled_weights an indicator for using scaled weights instead of regular weights</pre>
+                      <pre class="language-r">#' Basic Kaplan Meier (KM) plot function</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -14638,4119 +14479,6316 @@ <h2>maicplus coverage - 54.75%</h2>
                     <td class="num">250</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a plot of unscaled or scaled weights</pre>
+                      <pre class="language-r">#' This function can generate a basic KM plot with or without risk set table appended at the bottom. In a single plot,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">251</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' it can include up to 4 KM curves. This depends on number of levels in 'treatment' column in the input data.frame</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">252</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' \code{kmdat}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">253</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">plot_weights_base &lt;- function(weighted_data,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">254</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              bin_col, vline_col, main_title,</pre>
+                      <pre class="language-r">#' @param kmdat a `data.frame`, must consist `treatment`, `time` (unit in days), `n.risk`, `censor`, `surv`, similar to</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">255</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              scaled_weights) {</pre>
+                      <pre class="language-r">#'   an output from \code{maicplus:::survfit_makeup}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">256</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  weights_stat &lt;- calculate_weights_legend(weighted_data)</pre>
+                      <pre class="language-r">#' @param endpoint_name a string, name of time to event endpoint, to be show in the last line of title</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">257</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param time_scale a string, time unit of median survival time, taking a value of 'years', 'months', 'weeks' or 'days'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">258</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (scaled_weights) {</pre>
+                      <pre class="language-r">#' @param time_grid a numeric vector in the unit of \code{time_scale}, risk set table and x axis of the km plot will be</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">259</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    wt &lt;- weighted_data$data$scaled_weights</pre>
+                      <pre class="language-r">#'   defined based on this time grid</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">260</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    median_wt &lt;- weights_stat$wt_scaled_median</pre>
+                      <pre class="language-r">#' @param show_risk_set logical, show risk set table or not, TRUE by default</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">261</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">#' @param main_title a string, main title of the KM plot</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">262</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    wt &lt;- weighted_data$data$weights</pre>
+                      <pre class="language-r">#' @param subplot_heights a numeric vector, heights argument to \code{graphic::layout()},NULL by default which means</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">263</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    median_wt &lt;- weights_stat$wt_median</pre>
+                      <pre class="language-r">#'   user will use the default setting</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">264</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' @param suppress_plot_layout logical, suppress the layout setting in this function so that user can specify layout</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">265</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   outside of the function, FALSE by default</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">266</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # prepare legend</pre>
+                      <pre class="language-r">#' @param use_colors a character vector of length up to 4, colors to the KM curves, it will be passed to `col` of</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">267</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  plot_legend &lt;- c(</pre>
+                      <pre class="language-r">#'   \code{lines()}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">268</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    paste0("Median = ", median_wt),</pre>
+                      <pre class="language-r">#' @param use_line_types a numeric vector of length up to 4, line type to the KM curves, it will be passed to `lty` of</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">269</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    paste0("ESS = ", weights_stat$ess),</pre>
+                      <pre class="language-r">#'   \code{lines()}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">270</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    paste0("Reduction% = ", weights_stat$ess_reduct)</pre>
+                      <pre class="language-r">#' @param use_pch_cex a scalar between 0 and 1, point size to indicate censored individuals on the KM curves, it will be</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">271</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#'   passed to `cex` of \code{points()}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">272</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  plot_lty &lt;- c(2, NA, NA)</pre>
+                      <pre class="language-r">#' @param use_pch_alpha a scalar between 0 and 255, degree of color transparency of points to indicate censored</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">273</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   individuals on the KM curves, it will be passed to `cex` of \code{points()}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">274</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (weights_stat$nr_na &gt; 0) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">275</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    plot_legend &lt;- c(plot_legend, paste0("#Missing Weights = ", weights_stat$nr_na))</pre>
+                      <pre class="language-r">#' @example inst/examples/basic_kmplot_ex.R</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">276</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    plot_lty &lt;- c(plot_lty, NA)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">277</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' @return a KM plot with or without risk set table appended at the bottom, with up to 4 KM curves</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">278</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">279</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # plot</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">280</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
+                      <pre class="language-r">basic_kmplot &lt;- function(kmdat,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">281</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  par(mgp = c(2.3, 0.5, 0), cex.axis = 0.9, cex.lab = 0.95, bty = "n")</pre>
+                      <pre class="language-r">                         endpoint_name = "Time to Event Endpoint",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">282</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  on.exit(par(original_par))</pre>
+                      <pre class="language-r">                         time_scale,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">283</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  hist(wt, border = "white", col = bin_col, main = main_title, breaks = 20, yaxt = "n", xlab = "")</pre>
+                      <pre class="language-r">                         time_grid,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">284</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  axis(2, las = 1)</pre>
+                      <pre class="language-r">                         show_risk_set = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">285</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  abline(v = median(wt), lty = 2, col = vline_col, lwd = 2)</pre>
+                      <pre class="language-r">                         main_title = "Kaplan-Meier Curves",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">286</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  legend("topright", bty = "n", lty = plot_lty, cex = 0.8, legend = plot_legend)</pre>
+                      <pre class="language-r">                         subplot_heights = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">287</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">                         suppress_plot_layout = FALSE,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">288</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                         use_colors = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">289</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Plot MAIC weights in a histogram with key statistics in legend using `ggplot2`</pre>
+                      <pre class="language-r">                         use_line_types = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">290</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                         use_pch_cex = 0.65,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">291</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Generates a `ggplot` histogram of weights. Default is to plot both unscaled and scaled weights on a same graph.</pre>
+                      <pre class="language-r">                         use_pch_alpha = 100) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">292</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">293</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param weighted_data object returned after calculating weights using [estimate_weights]</pre>
+                      <pre class="language-r">  on.exit(par(original_par))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">294</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param bin_col a string, color for the bins of histogram</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">295</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param vline_col a string, color for the vertical line in the histogram</pre>
+                      <pre class="language-r">  # precheck</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">296</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param main_title Name of scaled weights plot and unscaled weights plot, respectively.</pre>
+                      <pre class="language-r">  if (!length(subplot_heights) %in% c(0, (1 + show_risk_set))) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">297</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param bins number of bin parameter to use</pre>
+                      <pre class="language-r">    stop("length of subplot_heights should be ", (1 + show_risk_set))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">298</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">299</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return a plot of unscaled and scaled weights</pre>
+                      <pre class="language-r">  if (!is.factor(kmdat$treatment)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">300</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">    stop("kmdat$treatment needs to be a factor, its levels will be used in legend and title, first level is comparator")</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">301</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">302</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">plot_weights_ggplot &lt;- function(weighted_data, bin_col, vline_col,</pre>
+                      <pre class="language-r">  if (nlevels(kmdat$treatment) &gt; 4) stop("kmdat$treatment cannot have more than 4 levels")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">303</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                main_title,</pre>
+                      <pre class="language-r">  if (is.null(time_grid) &amp;&amp; show_risk_set) stop("please provide a numeric vector as time_grid to show risk set table")</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">304</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                bins) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">305</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # check if ggplot2 package is installed</pre>
+                      <pre class="language-r">  # set up x axis (time)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">306</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!requireNamespace("ggplot2", quietly = TRUE)) {</pre>
+                      <pre class="language-r">  if (is.null(time_grid)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">307</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("ggplot2 package is needed to run this function")</pre>
+                      <pre class="language-r">    max_t &lt;- max(kmdat$time)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">308</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    t_range &lt;- c(0, get_time_as(max_t, time_scale) * 1.07)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">309</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">310</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  weights_stat &lt;- calculate_weights_legend(weighted_data)</pre>
+                      <pre class="language-r">    t_range &lt;- c(0, max(time_grid))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">311</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">312</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # prepare dataset to use in ggplot</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">313</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt_data0 &lt;- weighted_data$data[, c("weights", "scaled_weights")]</pre>
+                      <pre class="language-r">  # plat layout in par</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">314</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  colnames(wt_data0) &lt;- main_title</pre>
+                      <pre class="language-r">  if (!suppress_plot_layout) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">315</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt_data &lt;- stack(wt_data0)</pre>
+                      <pre class="language-r">    nr_subplot &lt;- (1 + show_risk_set)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">316</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  wt_data$median &lt;- ifelse(wt_data$ind == main_title[1],</pre>
+                      <pre class="language-r">    if (is.null(subplot_heights)) subplot_heights &lt;- c(7, 0.7 + nlevels(kmdat$treatment) * 0.7, 0.8)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">317</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    weights_stat$wt_median, weights_stat$wt_scaled_median</pre>
+                      <pre class="language-r">    layout_mat &lt;- matrix(1:nr_subplot, ncol = 1)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">318</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">    layout(layout_mat, heights = subplot_heights)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">319</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">320</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # create legend data</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">321</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  lab &lt;- with(weights_stat, {</pre>
+                      <pre class="language-r">  # plot cosmetic setup</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">322</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    lab &lt;- c(paste0("Median = ", wt_median), paste0("Median = ", wt_scaled_median))</pre>
+                      <pre class="language-r">  if (is.null(use_line_types)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">323</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    lab &lt;- paste0(lab, "\nESS = ", ess, "\nReduction% = ", ess_reduction)</pre>
+                      <pre class="language-r">    use_lty &lt;- c(1, 1, 2, 2)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">324</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (nr_na &gt; 0) lab &lt;- paste0(lab, "\n#Missing Weights = ", nr_na)</pre>
+                      <pre class="language-r">    use_lwd &lt;- c(1.5, 1.5, 1.2, 1.2)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">325</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    lab</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">326</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">    use_lty &lt;- use_line_types</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">327</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  legend_data &lt;- data.frame(ind = main_title, lab = lab)</pre>
+                      <pre class="language-r">    use_lwd &lt;- c(1.5, 1.5, 1.2, 1.2)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">328</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">329</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  hist_plot &lt;- ggplot2::ggplot(wt_data) +</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">330</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ggplot2::geom_histogram(ggplot2::aes_string(x = "values"), bins = bins, color = bin_col, fill = bin_col) +</pre>
+                      <pre class="language-r">  if (is.null(use_colors)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">331</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ggplot2::geom_vline(ggplot2::aes_string(xintercept = "median"),</pre>
+                      <pre class="language-r">    use_col &lt;- c("#5450E4", "#00857C", "#6ECEB2", "#7B68EE")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">332</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      color = vline_col,</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">333</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      linetype = "dashed"</pre>
+                      <pre class="language-r">    use_col &lt;- use_colors</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">334</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ) +</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">335</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ggplot2::theme_bw() +</pre>
+                      <pre class="language-r">  use_col2 &lt;- col2rgb(use_col) # preparing semi-transparent colors</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">336</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ggplot2::facet_wrap(~ind, ncol = 1) +</pre>
+                      <pre class="language-r">  use_col2 &lt;- rgb(use_col2[1, ], use_col2[2, ], use_col2[3, ], alpha = use_pch_alpha, maxColorValue = 255)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">337</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ggplot2::geom_text(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">338</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = legend_data,</pre>
+                      <pre class="language-r">  ## : first subplot: KM curve -------------------</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">339</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ggplot2::aes_string(label = "lab"), x = Inf, y = Inf, hjust = 1, vjust = 1, size = 3</pre>
+                      <pre class="language-r">  # base plot</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">340</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ) +</pre>
+                      <pre class="language-r">  par(bty = "n", tcl = -0.15, mgp = c(1.8, 0.4, 0), cex.lab = 0.85, cex.axis = 0.8, cex.main = 0.9, mar = c(3, 4, 5, 1))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">341</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ggplot2::theme(</pre>
+                      <pre class="language-r">  plot(0, 0,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">342</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      axis.title = ggplot2::element_text(size = 12),</pre>
+                      <pre class="language-r">    type = "n", xlab = paste0("Time in ", time_scale), ylab = "Survival Probability",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">343</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      axis.text = ggplot2::element_text(size = 12)</pre>
+                      <pre class="language-r">    ylim = c(0, 1), xlim = t_range, yaxt = "n", xaxt = "n",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">344</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    main = paste0(main_title, "\nEndpoint:", endpoint_name)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">345</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">346</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  axis(2, las = 1)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">347</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (!is.null(time_grid)) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">348</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    axis(1, at = time_grid)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">349</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  } else {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">350</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    axis(1)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">351</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  }</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">352</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">353</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # add km line</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">354</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  for (ii in 1:nlevels(kmdat$treatment)) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">355</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    tmpkmdat &lt;- kmdat[as.numeric(kmdat$treatment) == ii, , drop = FALSE]</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">356</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    lines(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">357</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      y = tmpkmdat$surv,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">358</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      x = get_time_as(tmpkmdat$time, time_scale),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">359</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      col = use_col[ii],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">360</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      lty = use_lty[ii],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">361</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      lwd = use_lwd[ii],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">362</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      type = "s"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">363</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">364</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    tmpid &lt;- (tmpkmdat$censor != 0) # cannot just ==1, anticipating weighted case</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">365</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    points(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">366</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      y = tmpkmdat$surv[tmpid],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">367</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      x = get_time_as(tmpkmdat$time[tmpid], time_scale),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">368</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      col = use_col2[ii],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">369</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      pch = 3,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">370</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      cex = use_pch_cex</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">371</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">372</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  }</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">373</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">374</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  ## : second subplot: risk set table (if applicable) -------------------</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">375</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (show_risk_set) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">376</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ) +</pre>
+                      <pre class="language-r">    # add legend, with treatment index</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">377</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    legend("topright",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">378</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      bty = "n",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">379</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      cex = 0.8,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">380</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      lty = use_lty[1:nlevels(kmdat$treatment)],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">381</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      lwd = use_lwd[1:nlevels(kmdat$treatment)],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">382</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      col = use_col[1:nlevels(kmdat$treatment)],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">383</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      legend = paste0("(T", 1:nlevels(kmdat$treatment), ") ", levels(kmdat$treatment))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">384</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">385</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">386</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    # add risk set table</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">387</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    par(bty = "n", tcl = -0.15, mgp = c(1.8, 0.4, 0), mar = c(1, 4, 0, 1))</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">388</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    plot(0, 0,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">389</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      type = "n", xlab = "", ylab = "", main = NULL,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">390</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      ylim = c(nlevels(kmdat$treatment) + 1.2, -0.5),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">391</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      xlim = t_range,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">392</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      yaxt = "n", xaxt = "n"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">393</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">394</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    axis(2,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">395</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      at = 1:nlevels(kmdat$treatment), labels = paste0("T", 1:nlevels(kmdat$treatment)),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">396</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      line = NA, lty = "blank", las = 1</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">397</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">398</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">399</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    for (ii in 1:nlevels(kmdat$treatment)) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">400</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      tmpkmdat &lt;- kmdat[as.numeric(kmdat$treatment) == ii, , drop = FALSE]</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">401</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      tmptime &lt;- get_time_as(tmpkmdat$time, time_scale)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">402</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      tmpnr &lt;- sapply(time_grid, function(kk) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">403</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        tmpid &lt;- which(tmptime &gt; kk)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">404</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        if (length(tmpid) == 0) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">405</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          if (min(tmpkmdat$n.risk) == 0) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">406</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">            tmpid &lt;- which.min(tmpkmdat$n.risk)[1]</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">407</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          } else {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">408</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">            tmpid &lt;- NULL</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">409</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          }</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">410</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        }</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">411</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        tout &lt;- ifelse(is.null(tmpid), "n/a", round(tmpkmdat$n.risk[tmpid], 1))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">412</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      })</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">413</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      text(0, 0, labels = "Number at risk", pos = 4, cex = 0.8, offset = -0.8)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">414</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      text(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">415</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        y = rep(ii, length(time_grid)),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">416</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        x = time_grid,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">417</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        labels = tmpnr,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">418</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        col = use_col[ii],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">419</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        cex = 0.75</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">420</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      )</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">421</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      text(0, nlevels(kmdat$treatment) + 1,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">422</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        pos = 4, cex = 0.7, offset = -0.8, col = "gray30",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">423</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        labels = "Note: Number at risk for adjusted/weighted treament arm is the sum of individual weight at risk."</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">424</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">425</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    }</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">426</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  } else {</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">427</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    # add simple</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">428</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    legend("topright",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">429</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      bty = "n",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">430</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      cex = 0.8,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">431</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      lty = use_lty[1:nlevels(kmdat$treatment)],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">432</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      lwd = use_lwd[1:nlevels(kmdat$treatment)],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">433</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      col = use_col[1:nlevels(kmdat$treatment)],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">434</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      legend = levels(kmdat$treatment)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">435</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">436</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  }</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">437</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">}</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">438</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">439</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">440</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' Diagnosis plot of proportional hazard assumption for anchored and unanchored</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">441</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">442</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param weights_object an object returned by \code{estimate_weight}</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">443</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param tte_ipd a data frame of individual patient data (IPD) of internal trial, contain at least "USUBJID", "EVENT",</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">444</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'   "TIME" columns and a column indicating treatment assignment</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">445</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param tte_pseudo_ipd a data frame of pseudo IPD by digitized KM curves of external trial (for time-to-event</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">446</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'   endpoint), contain at least "EVENT", "TIME"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">447</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param trt_ipd  a string, name of the interested investigation arm in internal trial \code{dat_igd} (real IPD)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">448</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param trt_agd a string, name of the interested investigation arm in external trial \code{dat_pseudo} (pseudo IPD)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">449</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param trt_common a string, name of the common comparator in internal and external trial, by default is NULL,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">450</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'   indicating unanchored case</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">451</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param trt_var_ipd a string, column name in \code{dat_ipd} that contains the treatment assignment</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">452</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param trt_var_agd a string, column name in \code{dat_ipd} that contains the treatment assignment</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">453</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param endpoint_name a string, name of time to event endpoint, to be show in the last line of title</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">454</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param time_scale a string, time unit of median survival time, taking a value of 'years', 'months', 'weeks' or 'days'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">455</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param zph_transform a string, pass to \code{survival::cox.zph}, default is "log"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">456</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param zph_log_hazard a logical, if TRUE (default), y axis of the time dependent hazard function is log-hazard,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">457</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'   otherwise, hazard.</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">458</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">459</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @return a 3 by 2 plot, include log-cumulative hazard plot, time dependent hazard function and unscaled Schoenfeld</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">460</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'   residual plot, before and after matching</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">461</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @export</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">462</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">ph_diagplot &lt;- function(weights_object,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">463</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        tte_ipd,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">464</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        tte_pseudo_ipd,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">465</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        trt_ipd,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">466</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        trt_agd,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">467</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        trt_common = NULL,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">468</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        trt_var_ipd = "ARM",</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">469</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        trt_var_agd = "ARM",</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">470</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        endpoint_name = "Time to Event Endpoint",</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">471</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        time_scale,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">472</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        zph_transform = "log",</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">473</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                        zph_log_hazard = TRUE) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">474</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  names(tte_ipd) &lt;- toupper(names(tte_ipd))</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">475</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  names(tte_pseudo_ipd) &lt;- toupper(names(tte_pseudo_ipd))</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">476</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  trt_var_ipd &lt;- toupper(trt_var_ipd)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">477</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  trt_var_agd &lt;- toupper(trt_var_agd)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">478</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">479</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # pre check</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">480</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (!"maicplus_estimate_weights" %in% class(weights_object)) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">481</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    stop("weights_object should be an object returned by estimate_weights")</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">482</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  }</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">483</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (!all(c("USUBJID", "TIME", "EVENT", trt_var_ipd) %in% names(tte_ipd))) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">484</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    stop("tte_ipd needs to include at least USUBJID, TIME, EVENT, ", trt_var_ipd)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">485</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  }</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">486</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (!all(c("TIME", "EVENT", trt_var_agd) %in% names(tte_pseudo_ipd))) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">487</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    stop("tte_ipd needs to include at least TIME, EVENT, ", trt_var_agd)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">488</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  }</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">489</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">490</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # preparing analysis data</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">491</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  is_anchored &lt;- ifelse(is.null(trt_common), FALSE, TRUE)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">492</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  tte_ipd &lt;- tte_ipd[tte_ipd[[trt_var_ipd]] %in% c(trt_ipd, trt_common), , drop = TRUE]</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">493</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  tte_pseudo_ipd &lt;- tte_pseudo_ipd[tte_pseudo_ipd[[trt_var_agd]] %in% c(trt_agd, trt_common), , drop = TRUE]</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">494</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  tte_ipd$weights &lt;- weights_object$data$weights[match(weights_object$data$USUBJID, tte_ipd$USUBJID)]</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">495</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  tte_pseudo_ipd$weights &lt;- 1</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">496</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  tte_ipd$TIME2 &lt;- get_time_as(tte_ipd$TIME, as = time_scale) # for cox.zph</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">497</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  tte_pseudo_ipd$TIME2 &lt;- get_time_as(tte_pseudo_ipd$TIME, as = time_scale) # for cox.zph</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">498</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (!"USUBJID" %in% names(tte_pseudo_ipd)) tte_pseudo_ipd$USUBJID &lt;- paste0("ID", seq_len(nrow(tte_pseudo_ipd)))</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">499</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (trt_var_ipd != "ARM") tte_ipd$ARM &lt;- tte_ipd[[trt_var_ipd]]</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">500</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (trt_var_agd != "ARM") tte_pseudo_ipd$ARM &lt;- tte_pseudo_ipd[[trt_var_agd]]</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">501</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">502</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # prepare plot data</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">503</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  retain_cols &lt;- c("USUBJID", "TIME", "TIME2", "EVENT", "ARM", "weights")</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">504</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (!is_anchored) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">505</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    # unanchored case</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">506</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    tte_dat &lt;- rbind(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">507</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      tte_ipd[, retain_cols, drop = FALSE],</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">508</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      tte_pseudo_ipd[, retain_cols, drop = FALSE]</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">509</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">510</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  } else {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">511</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    tte_dat &lt;- tte_ipd[, retain_cols, drop = FALSE]</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">512</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  }</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">513</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  kmobj &lt;- survival::survfit(Surv(TIME, EVENT) ~ ARM, tte_dat, conf.type = "log-log")</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">514</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  kmobj_adj &lt;- survival::survfit(Surv(TIME, EVENT) ~ ARM, tte_dat, conf.type = "log-log", weights = weights)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">515</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  coxobj &lt;- survival::coxph(Surv(TIME, EVENT) ~ ARM, data = tte_dat)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">516</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  coxobj2 &lt;- survival::coxph(Surv(TIME2, EVENT) ~ ARM, data = tte_dat)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">517</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  zphobj &lt;- survival::cox.zph(coxobj2, transform = zph_transform, global = FALSE)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">518</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  coxobj_adj &lt;- survival::coxph(Surv(TIME, EVENT) ~ ARM, data = tte_dat, weights = weights)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">519</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  coxobj_adj2 &lt;- survival::coxph(Surv(TIME2, EVENT) ~ ARM, data = tte_dat, weights = weights)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">520</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  zphobj_adj &lt;- survival::cox.zph(coxobj_adj2, transform = zph_transform, global = FALSE)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">521</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">522</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # making the plot</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">523</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">524</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  par(mfrow = c(3, 2), cex.lab = 0.85, cex.axis = 0.8, cex.main = 0.9)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">525</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  on.exit(par(original_par))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">526</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # log-cum-hazard plot</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">527</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  ph_diagplot_lch(kmobj,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">528</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    time_scale = time_scale,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">529</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    log_time = TRUE,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">530</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    endpoint_name = endpoint_name,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">531</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    subtitle = "(Before Matching)"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">532</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">533</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">534</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  ph_diagplot_lch(kmobj_adj,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">535</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    time_scale = time_scale,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">536</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    log_time = TRUE,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">537</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    endpoint_name = endpoint_name,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">538</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    subtitle = "(After Matching)"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">539</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">540</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # time dependent hazard plot</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">541</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  plot(zphobj,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">542</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    main = paste0(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">543</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      "Time-dependent Hazard function (scaled Schoenfeld residual)\n",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">544</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      "Endpoint:", endpoint_name, "\n(Before Matching)"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">545</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    ),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">546</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    resid = FALSE, se = TRUE, df = 4, nsmo = 40,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">547</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    # xlim = range(0,zphobj$time),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">548</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    ylab = ifelse(zph_log_hazard, "Log Hazard", "Hazard"),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">549</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    xlab = paste("Time in", time_scale),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">550</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    lty = 1:2, lwd = 2, pch = 16, cex = 0.8,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">551</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    col = rgb(0, 0, 128, alpha = 120, maxColorValue = 255),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">552</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    hr = (!zph_log_hazard), yaxt = "n"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">553</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">554</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  axis(2, las = 1)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">555</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  pv &lt;- as.data.frame(zphobj$table)$p</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">556</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  pv &lt;- ifelse(round(pv, 4) &lt; 0.0001, "&lt;0.0001", format(round(pv, 4), nsmall = 4))</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">557</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  legend("bottomright",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">558</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    cex = 0.75, bty = "n", text.col = "dodgerblue3",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">559</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    legend = c(paste0("p-value: ", pv), paste0("time-transform: ", zph_transform)),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">560</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    title = "PH test (survival::cox.zph)"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">561</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">562</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">563</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  plot(zphobj_adj,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">564</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    main = paste0(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">565</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      "Time-dependent Hazard function (scaled Schoenfeld residual)\n",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">566</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      "Endpoint:", endpoint_name, "\n(After Matching)"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">567</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    ),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">568</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    resid = FALSE, se = TRUE, df = 4, nsmo = 40,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">569</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    # xlim = range(0,zphobj$time),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">570</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    ylab = ifelse(zph_log_hazard, "Log Hazard", "Hazard"),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">571</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    xlab = paste("Time in", time_scale),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">572</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    lty = 1:2, lwd = 2, pch = 16, cex = 0.8,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">573</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    col = rgb(0, 0, 128, alpha = 120, maxColorValue = 255),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">574</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    hr = (!zph_log_hazard), yaxt = "n"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">575</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">576</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  axis(2, las = 1)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">577</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  pv &lt;- as.data.frame(zphobj_adj$table)$p</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">578</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  pv &lt;- ifelse(round(pv, 4) &lt; 0.0001, "&lt;0.0001", format(round(pv, 4), nsmall = 4))</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">579</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  legend("bottomright",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">580</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    cex = 0.75, bty = "n", text.col = "dodgerblue3",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">581</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    legend = c(paste0("p-value: ", pv), paste0("time-transform: ", zph_transform)),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">582</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    title = "PH test (survival::cox.zph)"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">583</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">584</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">585</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  # unscaled schoenfeld residual</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">586</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  ph_diagplot_schoenfeld(coxobj,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">587</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    time_scale = time_scale,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">588</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    log_time = FALSE,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">589</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    endpoint_name = endpoint_name,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">590</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    subtitle = "(Before Matching)"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">591</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">592</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">593</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  ph_diagplot_schoenfeld(coxobj_adj,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">594</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    time_scale = time_scale,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">595</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    log_time = FALSE,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">596</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    endpoint_name = endpoint_name,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">597</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    subtitle = "(After Matching)"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">598</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">599</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">}</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">600</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">601</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' PH Diagnosis Plot of Log Cumulative Hazard Rate versus time or log-time</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">602</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">603</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' This plot is also known as log negative log survival rate.</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">604</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">605</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' a diagnosis plot for proportional hazard assumption, versus log-time (default) or time</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">606</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">607</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param km_fit returned object from \code{survival::survfit}</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">608</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param time_scale a character string, 'years', 'months', 'weeks' or 'days', time unit of median survival time</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">609</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param log_time logical, TRUE (default) or FALSE</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">610</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param endpoint_name a character string, name of the endpoint</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">611</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param subtitle a character string, subtitle of the plot</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">612</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @param exclude_censor logical, should censored data point be plotted</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">613</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @examples</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">614</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' library(survival)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">615</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' load(system.file("extdata", "combined_data_tte.rda", package = "maicplus", mustWork = TRUE))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">616</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' kmobj &lt;- survfit(Surv(TIME, EVENT) ~ ARM, combined_data_tte, conf.type = "log-log")</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">617</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' ph_diagplot_lch(kmobj,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">618</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'   time_scale = "month", log_time = TRUE,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">619</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'   endpoint_name = "OS", subtitle = "(Before Matching)"</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">620</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">621</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @return a plot of log cumulative hazard rate</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">622</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @export</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">623</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">624</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">ph_diagplot_lch &lt;- function(km_fit,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">625</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                            time_scale,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">626</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                            log_time = TRUE,</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">627</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                            endpoint_name = "",</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">628</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                            subtitle = "",</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">629</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">                            exclude_censor = TRUE) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">630</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  time_scale &lt;- match.arg(arg = time_scale, choices = c("days", "weeks", "months", "years"))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">631</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">632</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  clldat &lt;- survfit_makeup(km_fit)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">633</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">634</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (exclude_censor) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">635</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    clldat &lt;- lapply(clldat, function(xxt) xxt[xxt$censor == 0, , drop = FALSE])</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">636</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  }</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">637</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">638</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  all.times &lt;- get_time_as(do.call(rbind, clldat)$time, time_scale)</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">639</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (log_time) all.times &lt;- log(all.times)</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">640</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  t_range &lt;- range(all.times)</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">641</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  y_range &lt;- range(log(do.call(rbind, clldat)$cumhaz))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">642</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">643</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">644</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  par(mar = c(4, 4, 4, 1), bty = "n", tcl = -0.15, mgp = c(1.5, 0.3, 0))</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">645</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  on.exit(par(original_par))</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">646</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  plot(0, 0,</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">647</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    type = "n", xlab = paste0(ifelse(log_time, "Log-", ""), "Time in ", time_scale),</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">648</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    ylab = "Log-Cumulative Hazard Rate",</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">649</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    ylim = y_range, xlim = t_range, yaxt = "n",</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">650</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    main = paste0(</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">651</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      "Log Cumulative Hazard versus Log Time\nEndpoint: ", endpoint_name,</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">652</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      ifelse(subtitle == "", "", "\n"), subtitle</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">653</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">654</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">655</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  axis(2, las = 1)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">656</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">657</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  trts &lt;- names(clldat)</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">658</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  cols &lt;- c("dodgerblue3", "firebrick3")</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">659</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  pchs &lt;- c(1, 4)</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">660</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  for (i in seq_along(clldat)) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">661</td>
+                    <td class="coverage">4<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    use_x &lt;- get_time_as(clldat[[i]]$time, time_scale)</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">662</td>
+                    <td class="coverage">4<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    if (log_time) use_x &lt;- log(use_x)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">663</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">664</td>
+                    <td class="coverage">4<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    lines(</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">665</td>
+                    <td class="coverage">4<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      y = log(clldat[[i]]$cumhaz),</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">666</td>
+                    <td class="coverage">4<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      x = use_x, col = cols[i],</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">667</td>
+                    <td class="coverage">4<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      type = "s",</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">668</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">669</td>
+                    <td class="coverage">4<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    points(</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">670</td>
+                    <td class="coverage">4<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      y = log(clldat[[i]]$cumhaz),</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">671</td>
+                    <td class="coverage">4<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      x = use_x,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">345</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">672</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ggplot2::ylab("Frequency") +</pre>
+                      <pre class="language-r">      col = cols[i], pch = pchs[i], cex = 0.7</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">346</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">673</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ggplot2::xlab("Weight")</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">347</td>
+                    <td class="num">674</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">348</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">675</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  return(hist_plot)</pre>
+                      <pre class="language-r">  legend("bottomright",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">349</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">676</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">    bty = "n", lty = c(1, 1, 2), cex = 0.8,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">350</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">677</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    col = cols, pch = pchs, legend = paste0("Treatment: ", trts)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">351</td>
+                    <td class="num">678</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">352</td>
+                    <td class="num">679</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Plot method for Estimate Weights objects</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">353</td>
+                    <td class="num">680</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">354</td>
+                    <td class="num">681</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' The plot function displays individuals weights with key summary in top right legend that includes</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">355</td>
+                    <td class="num">682</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' median weight, effective sample size (ESS), and reduction percentage (what percent ESS is reduced from the</pre>
+                      <pre class="language-r">#' PH Diagnosis Plot of Schoenfeld residuals for a Cox model fit</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">356</td>
+                    <td class="num">683</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' original sample size). There are two options of plotting: base R plot and `ggplot`. The default</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">357</td>
+                    <td class="num">684</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' for base R plot is to plot unscaled and scaled separately. The default</pre>
+                      <pre class="language-r">#' @param coxobj object returned from \code{\link[survival]{coxph}}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">358</td>
+                    <td class="num">685</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' for `ggplot` is to plot unscaled and scaled weights on a same plot.</pre>
+                      <pre class="language-r">#' @param time_scale a character string, 'years', 'months', 'weeks' or 'days', time unit of median survival time</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">359</td>
+                    <td class="num">686</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @param log_time logical, TRUE (default) or FALSE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">360</td>
+                    <td class="num">687</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param x object from [estimate_weights]</pre>
+                      <pre class="language-r">#' @param endpoint_name a character string, name of the endpoint</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">361</td>
+                    <td class="num">688</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ggplot indicator to print base weights plot or `ggplot` weights plot</pre>
+                      <pre class="language-r">#' @param subtitle a character string, subtitle of the plot</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">362</td>
+                    <td class="num">689</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param bin_col a string, color for the bins of histogram</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">363</td>
+                    <td class="num">690</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param vline_col a string, color for the vertical line in the histogram</pre>
+                      <pre class="language-r">#' library(survival)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">364</td>
+                    <td class="num">691</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param main_title title of the plot. For ggplot, name of scaled weights plot and unscaled weights plot, respectively.</pre>
+                      <pre class="language-r">#' load(system.file("extdata", "combined_data_tte.rda", package = "maicplus", mustWork = TRUE))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">365</td>
+                    <td class="num">692</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param scaled_weights (base plot only) an indicator for using scaled weights instead of regular weights</pre>
+                      <pre class="language-r">#' unweighted_cox &lt;- coxph(Surv(TIME, EVENT == 1) ~ ARM, data = combined_data_tte)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">366</td>
+                    <td class="num">693</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param bins (`ggplot` only) number of bin parameter to use</pre>
+                      <pre class="language-r">#' ph_diagplot_schoenfeld(unweighted_cox,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">367</td>
+                    <td class="num">694</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   time_scale = "month", log_time = TRUE,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">368</td>
+                    <td class="num">695</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">#'   endpoint_name = "OS", subtitle = "(Before Matching)"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">369</td>
+                    <td class="num">696</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' plot(weighted_sat)</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">370</td>
+                    <td class="num">697</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @return a plot of Schoenfeld residuals</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">371</td>
+                    <td class="num">698</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (requireNamespace("ggplot2")) {</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">372</td>
+                    <td class="num">699</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   plot(weighted_sat, ggplot = TRUE)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">373</td>
+                    <td class="num">700</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">ph_diagplot_schoenfeld &lt;- function(coxobj,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">374</td>
+                    <td class="num">701</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn estimate_weights Plot method for estimate_weights objects</pre>
+                      <pre class="language-r">                                   time_scale = "months",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">375</td>
+                    <td class="num">702</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">                                   log_time = TRUE,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">376</td>
+                    <td class="num">703</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                                   endpoint_name = "",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">377</td>
+                    <td class="num">704</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">plot.maicplus_estimate_weights &lt;- function(x, ggplot = FALSE,</pre>
+                      <pre class="language-r">                                   subtitle = "") {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">378</td>
+                    <td class="num">705</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                           bin_col = "#6ECEB2", vline_col = "#688CE8",</pre>
+                      <pre class="language-r">  # pre-check</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">379</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">706</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                           main_title = NULL,</pre>
+                      <pre class="language-r">  time_scale &lt;- match.arg(arg = time_scale, choices = c("days", "weeks", "months", "years"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">380</td>
+                    <td class="num">707</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                           scaled_weights = TRUE,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">381</td>
+                    <td class="num">708</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                           bins = 50, ...) {</pre>
+                      <pre class="language-r">  # prepare data</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">382</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">709</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (ggplot) {</pre>
+                      <pre class="language-r">  schresid &lt;- residuals(coxobj, type = "schoenfeld")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">383</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">710</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (is.null(main_title)) main_title &lt;- c("Scaled Individual Weights", "Unscaled Individual Weights")</pre>
+                      <pre class="language-r">  plot_x &lt;- get_time_as(as.numeric(names(schresid)), time_scale)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">384</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">711</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    plot_weights_ggplot(x, bin_col, vline_col, main_title, bins)</pre>
+                      <pre class="language-r">  if (log_time) plot_x &lt;- log(plot_x)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">385</td>
+                    <td class="num">712</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">386</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    if (is.null(main_title)) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">387</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      main_title &lt;- ifelse(scaled_weights, "Scaled Individual Weights", "Unscaled Individual Weights")</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">388</td>
+                    <td class="num">713</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">  # loewss fit</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">389</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">714</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    plot_weights_base(x, bin_col, vline_col, main_title, scaled_weights)</pre>
+                      <pre class="language-r">  fit0 &lt;- predict(loess(schresid ~ plot_x), se = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">390</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">715</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  uppband &lt;- fit0$fit + qt(0.975, fit0$df) * fit0$se</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">391</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">716</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  lowband &lt;- fit0$fit - qt(0.975, fit0$df) * fit0$se</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">392</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">717</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  use_yrange &lt;- range(schresid, uppband, lowband)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">393</td>
+                    <td class="num">718</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">394</td>
+                    <td class="num">719</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Check to see if weights are optimized correctly</pre>
+                      <pre class="language-r">  # making the plot</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">395</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">720</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  original_par &lt;- par(no.readonly = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">396</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">721</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This function checks to see if the optimization is done properly by checking the covariate averages</pre>
+                      <pre class="language-r">  par(bty = "n", mar = c(4, 4, 4, 1), tcl = -0.15, mgp = c(1.5, 0.3, 0))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">397</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">722</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' before and after adjustment.</pre>
+                      <pre class="language-r">  on.exit(par(original_par))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">398</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">723</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  plot(schresid ~ plot_x,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">399</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">724</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param weighted_data object returned after calculating weights using \code{\link{estimate_weights}}</pre>
+                      <pre class="language-r">    type = "n",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">400</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">725</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param processed_agd a data frame, object returned after using \code{\link{process_agd}} or</pre>
+                      <pre class="language-r">    yaxt = "n", ylim = use_yrange,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">401</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">726</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' aggregated data following the same naming convention</pre>
+                      <pre class="language-r">    ylab = "Unscaled Schoenfeld Residual",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">402</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">727</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    xlab = paste0(ifelse(log_time, "Log-", ""), "Time in ", time_scale),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">403</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">728</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">    main = paste0(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">404</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">729</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' check_weights(weighted_sat, process_agd(agd))</pre>
+                      <pre class="language-r">      "Unscaled Schoenfeld Residual\nEndpoint: ", endpoint_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">405</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">730</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      ifelse(subtitle == "", "", "\n"), subtitle</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">406</td>
+                    <td class="num">731</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @import DescTools</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">407</td>
+                    <td class="num">732</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">408</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">733</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return data.frame of weighted and unweighted covariate averages of the IPD,</pre>
+                      <pre class="language-r">  axis(2, las = 1)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">409</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">734</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' average of aggregate data, and sum of inner products of covariate \eqn{x_i} and the weights (\eqn{exp(x_i\beta)})</pre>
+                      <pre class="language-r">  lines(fit0$fit ~ plot_x, lty = 2, lwd = 1, col = rgb(0, 0, 128, 150, maxColorValue = 255))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">410</td>
+                    <td class="num">735</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">  # lines(uppband ~ plot_x, lty =2, lwd=1, col = rgb(0,0,128,120,maxColorValue = 255))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">411</td>
+                    <td class="num">736</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # lines(lowband ~ plot_x, lty =2, lwd=1, col = rgb(0,0,128,120,maxColorValue = 255))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">412</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">737</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">check_weights &lt;- function(weighted_data, processed_agd) {</pre>
+                      <pre class="language-r">  polygon(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">413</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">738</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ipd_with_weights &lt;- weighted_data$data</pre>
+                      <pre class="language-r">    x = c(plot_x, rev(plot_x)),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">414</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">739</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  match_cov &lt;- weighted_data$centered_colnames</pre>
+                      <pre class="language-r">    y = c(uppband, rev(lowband)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">415</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">740</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    col = rgb(0, 0, 128, 60, maxColorValue = 255),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">416</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">741</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # if algorithm is correct, all centered columns should have a weighted summation to a very small number around zero</pre>
+                      <pre class="language-r">    border = NA</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">417</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">742</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  num_check &lt;- ipd_with_weights$weights %*% as.matrix(ipd_with_weights[, match_cov, drop = FALSE])</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">418</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">743</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  num_check &lt;- round(num_check, 4)</pre>
+                      <pre class="language-r">  abline(h = 0, lty = 1, lwd = 1, col = "deeppink")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">419</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">744</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  points(schresid ~ plot_x,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">420</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">745</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # for reporting</pre>
+                      <pre class="language-r">    pch = 16,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">421</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">746</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  outdata &lt;- data.frame(</pre>
+                      <pre class="language-r">    cex = 0.85,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">422</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">747</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    covariate = gsub("_CENTERED$", "", match_cov),</pre>
+                      <pre class="language-r">    col = rgb(169, 169, 169, 120, maxColorValue = 255)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">423</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">748</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    match_stat = NA,</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">424</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">749</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    internal_trial = NA,</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">425</td>
-                    <td class="coverage">!</td>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/bucher.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
+                  <tr class="never">
+                    <td class="num">1</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    internal_trial_after_weighted = NA,</pre>
+                      <pre class="language-r">#' Bucher method for combining treatment effects</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">426</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">2</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    external_trial = NA,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">427</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    sum_centered_IPD_with_weights = as.vector(num_check)</pre>
+                      <pre class="language-r">#' Given two treatment effects of A vs. C and B vs. C</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">428</td>
+                    <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#' derive the treatment effects of A vs. B using the Bucher method.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">429</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">5</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  attr(outdata, "footer") &lt;- list()</pre>
+                      <pre class="language-r">#' Two-sided confidence interval and Z-test p-value are also calculated.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">430</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # find item that was matched by mean</pre>
+                      <pre class="language-r">#' Treatment effects and standard errors should be in log scale</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">431</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">7</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ind_mean &lt;- lapply(outdata$covariate, grep, x = names(processed_agd), value = TRUE)</pre>
+                      <pre class="language-r">#' for hazard ratio, odds ratio, and risk ratio.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">432</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">8</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ind_mean &lt;- sapply(ind_mean, function(ii) any(grepl("_MEAN$", ii)))</pre>
+                      <pre class="language-r">#' Treatment effects and standard errors should be in natural scale</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">433</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">9</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  outdata$match_stat &lt;- ifelse(grepl("_MEDIAN$", outdata$covariate), "Median",</pre>
+                      <pre class="language-r">#' for risk difference and mean difference.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">434</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">10</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ifelse(grepl("_SQUARED$", outdata$covariate), "SD",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">435</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">11</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ifelse(ind_mean, "Mean", "Prop")</pre>
+                      <pre class="language-r">#' @param trt a list of two scalars for the study with the</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">436</td>
+                    <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' experimental arm. `'est'` is the point estimate and `'se'`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">437</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#' is the standard error of the treatment effect.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">438</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">14</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  outdata$covariate &lt;- gsub("_MEDIAN|_SQUARED", "", outdata$covariate)</pre>
+                      <pre class="language-r">#' For time-to-event data, `'est'` and `'se'` should be point estimate and</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">439</td>
+                    <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # fill in corresponding agd data</pre>
+                      <pre class="language-r">#' standard error of the log hazard ratio.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">440</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">16</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  outdata$external_trial &lt;- unlist(processed_agd[paste(outdata$covariate, toupper(outdata$match_stat), sep = "_")])</pre>
+                      <pre class="language-r">#' For binary data, `'est'` and `'se'` should be point estimate and</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">441</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' standard error of the log odds ratio, log risk ratio, or risk</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">442</td>
+                    <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # fill in stat from unweighted and weighted IPD</pre>
+                      <pre class="language-r">#' difference.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">443</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">19</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  for (ii in seq_len(nrow(outdata))) {</pre>
+                      <pre class="language-r">#' For continuous data,  `'est'` and `'se'` should be point estimate and</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">444</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">20</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    covname &lt;- outdata$covariate[ii]</pre>
+                      <pre class="language-r">#' standard error of the mean difference.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">445</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">21</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (outdata$match_stat[ii] %in% c("Mean", "Prop")) {</pre>
+                      <pre class="language-r">#' @param com same as \code{trt}, but for the study with the</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">446</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">22</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      outdata$internal_trial[ii] &lt;- mean(ipd_with_weights[[covname]], na.rm = TRUE)</pre>
+                      <pre class="language-r">#' control arm</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">447</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">23</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      outdata$internal_trial_after_weighted[ii] &lt;- weighted.mean(</pre>
+                      <pre class="language-r">#' @param conf_lv a numerical scalar, prescribe confidence level to derive</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">448</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">24</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ipd_with_weights[[covname]],</pre>
+                      <pre class="language-r">#' two-sided confidence interval for the treatment effect</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">449</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">25</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        w = ipd_with_weights$weights, na.rm = TRUE</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">450</td>
+                    <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' @return a list with 5 elements,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">451</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">27</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    } else if (outdata$match_stat[ii] == "Median") {</pre>
+                      <pre class="language-r">#' \describe{</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">452</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">28</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      outdata$internal_trial[ii] &lt;- quantile(ipd_with_weights[[covname]],</pre>
+                      <pre class="language-r">#'   \item{est}{a scalar, point estimate of the treatment effect}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">453</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">29</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        probs = 0.5,</pre>
+                      <pre class="language-r">#'   \item{se}{a scalar, standard error of the treatment effect}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">454</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">30</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        na.rm = TRUE,</pre>
+                      <pre class="language-r">#'   \item{ci_l}{a scalar, lower confidence limit of a two-sided CI</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">455</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">31</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        type = 2,</pre>
+                      <pre class="language-r">#'   with prescribed nominal level by \code{conf_lv}}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">456</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">32</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        names = FALSE</pre>
+                      <pre class="language-r">#'   \item{ci_u}{a scalar, upper confidence limit of a two-sided CI</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">457</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">33</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ) # SAS default</pre>
+                      <pre class="language-r">#'   with prescribed nominal level by \code{conf_lv}}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">458</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">34</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      outdata$internal_trial_after_weighted[ii] &lt;- DescTools::Quantile(ipd_with_weights[[covname]],</pre>
+                      <pre class="language-r">#'   \item{pval}{p-value of Z-test, with null hypothesis that</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">459</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">35</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        weights = ipd_with_weights$weights,</pre>
+                      <pre class="language-r">#'   \code{est} is zero}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">460</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">36</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        probs = 0.5,</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">461</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">37</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        na.rm = TRUE,</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">462</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">38</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        type = 5,</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">463</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">39</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        names = FALSE</pre>
+                      <pre class="language-r">#' trt &lt;- list(est = log(1.1), se = 0.2)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">464</td>
+                    <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' com &lt;- list(est = log(1.3), se = 0.18)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">465</td>
+                    <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # no IPD equals to reported AgD median</pre>
+                      <pre class="language-r">#' result &lt;- bucher(trt, com, conf_lv = 0.9)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">466</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">42</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      msg_ind &lt;- !any(ipd_with_weights[[covname]] == outdata$external_trial[ii], na.rm = TRUE)</pre>
+                      <pre class="language-r">#' print(result, ci_digits = 3, pval_digits = 3)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">467</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">43</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (msg_ind) {</pre>
+                      <pre class="language-r">bucher &lt;- function(trt, com, conf_lv = 0.95) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">468</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">44</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        msg_txt &lt;- paste0(</pre>
+                      <pre class="language-r">  if (!isTRUE(is.finite(trt$est))) stop("trt$est is not valid: ", trt$est)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">469</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">45</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "For covariate ", covname, ", it was matched to AgD median, but there is no IPD identical to AgD median,",</pre>
+                      <pre class="language-r">  if (!isTRUE(is.finite(trt$se))) stop("trt$se is not valid: ", trt$se)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">470</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">46</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "hence median after weighted will not equal to AgD median exactly."</pre>
+                      <pre class="language-r">  if (!isTRUE(is.finite(com$est))) stop("com$est is not valid: ", com$est)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">471</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">47</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">  if (!isTRUE(is.finite(com$se))) stop("com$se is not valid: ", com$se)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">472</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">48</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        attr(outdata, "footer") &lt;- c(attr(outdata, "footer"), msg_txt)</pre>
+                      <pre class="language-r">  if (conf_lv &lt; 0 || 1 &lt; conf_lv) stop("conf_lv must be in (0, 1): ", conf_lv)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">473</td>
+                    <td class="num">49</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">474</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">50</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    } else if (outdata$match_stat[ii] == "SD") {</pre>
+                      <pre class="language-r">  est &lt;- trt$est - com$est</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">475</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">51</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      outdata$internal_trial[ii] &lt;- sd(ipd_with_weights[[covname]], na.rm = TRUE)</pre>
+                      <pre class="language-r">  se &lt;- sqrt(trt$se^2 + com$se^2)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">476</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">52</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      wm_squared &lt;- weighted.mean(ipd_with_weights[[covname]]^2, w = ipd_with_weights$weights, na.rm = TRUE)</pre>
+                      <pre class="language-r">  ci_l &lt;- est - stats::qnorm(0.5 + conf_lv / 2) * se</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">477</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">53</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ms_agd &lt;- processed_agd[[paste0(outdata$covariate[ii], "_MEAN")]]^2</pre>
+                      <pre class="language-r">  ci_u &lt;- est + stats::qnorm(0.5 + conf_lv / 2) * se</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">478</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">54</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      outdata$internal_trial_after_weighted[ii] &lt;- sqrt(wm_squared - ms_agd)</pre>
+                      <pre class="language-r">  if (est &gt; 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">479</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">55</td>
+                    <td class="coverage">42<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">    pval &lt;- 2 * (1 - stats::pnorm(est, 0, se))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">480</td>
+                    <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">481</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">57</td>
+                    <td class="coverage">71<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    pval &lt;- 2 * stats::pnorm(est, 0, se)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">482</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # output</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">483</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  class(outdata) &lt;- c("maicplus_check_weights", "data.frame")</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">484</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  outdata</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">485</td>
+                    <td class="num">59</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">486</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">60</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  outdata &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">487</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">61</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    est = est,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">488</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">62</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Print method for Check Weights objects</pre>
+                      <pre class="language-r">    se = se,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">489</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">63</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    ci_l = ci_l,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">490</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">64</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param x object from [check_weights]</pre>
+                      <pre class="language-r">    ci_u = ci_u,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">491</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">65</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param mean_digits number of digits for rounding mean columns in the output</pre>
+                      <pre class="language-r">    pval = pval</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">492</td>
+                    <td class="num">66</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param prop_digits number of digits for rounding proportion columns in the output</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">493</td>
+                    <td class="num">67</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param sd_digits number of digits for rounding mean columns in the output</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">494</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">68</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param digits minimal number of significant digits, see [print.default].</pre>
+                      <pre class="language-r">  class(outdata) &lt;- c("maicplus_bucher", "list")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">495</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">69</td>
+                    <td class="coverage">113<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ... further arguments to [print.data.frame]</pre>
+                      <pre class="language-r">  outdata</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">496</td>
+                    <td class="num">70</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn check_weights Print method for check_weights objects</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">497</td>
+                    <td class="num">71</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">498</td>
+                    <td class="num">72</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">499</td>
+                    <td class="num">73</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">print.maicplus_check_weights &lt;- function(x,</pre>
+                      <pre class="language-r">#' Calculate standard error from the reported confidence interval.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">500</td>
+                    <td class="num">74</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                         mean_digits = 2,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">501</td>
+                    <td class="num">75</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                         prop_digits = 2,</pre>
+                      <pre class="language-r">#' Comparator studies often only report confidence interval of the</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">502</td>
+                    <td class="num">76</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                         sd_digits = 3,</pre>
+                      <pre class="language-r">#' treatment effects. This function calculates standard error of the</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">503</td>
+                    <td class="num">77</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                         digits = getOption("digits"), ...) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">504</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  round_digits &lt;- c("Mean" = mean_digits, "Prop" = prop_digits, "SD" = sd_digits)[x$match_stat]</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">505</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  round_digits[is.na(round_digits)] &lt;- digits</pre>
+                      <pre class="language-r">#' treatment effect given the reported confidence interval.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">506</td>
+                    <td class="num">78</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' For relative treatment effect (i.e. hazard ratio, odds ratio, and</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">507</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">79</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  x$external_trial &lt;- round(x$external_trial, round_digits)</pre>
+                      <pre class="language-r">#' risk ratio), the function would log the confidence interval.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">508</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">80</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  x$internal_trial &lt;- round(x$internal_trial, round_digits)</pre>
+                      <pre class="language-r">#' For risk difference and mean difference,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">509</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">81</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  x$internal_trial_after_weighted &lt;- round(x$internal_trial_after_weighted, round_digits)</pre>
+                      <pre class="language-r">#' we do not log the confidence interval.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">510</td>
+                    <td class="num">82</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' The option to log the confidence interval is controlled</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">511</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">83</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  print.data.frame(x, ...)</pre>
+                      <pre class="language-r">#' by `'logged'` parameter.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">512</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">84</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  footer &lt;- unlist(attr(x, "footer"))</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">513</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">85</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (length(footer)) {</pre>
+                      <pre class="language-r">#' @param CI_lower Reported lower percentile value of the</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">514</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">86</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    cat("\n")</pre>
+                      <pre class="language-r">#' treatment effect</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">515</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">87</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    for (f in seq_along(footer)) {</pre>
+                      <pre class="language-r">#' @param CI_upper Reported upper percentile value of the</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">516</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">88</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      cat(paste0("[", f, "] ", footer[f]))</pre>
+                      <pre class="language-r">#' treatment effect</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">517</td>
+                    <td class="num">89</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">#' @param CI_perc Percentage of confidence interval reported</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">518</td>
+                    <td class="num">90</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' @param logged Whether the confidence interval should be logged.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">519</td>
+                    <td class="num">91</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#' For relative treatment effect, log should be applied because</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">520</td>
+                    <td class="num">92</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' estimated log treatment effect is approximately normally distributed.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">521</td>
+                    <td class="num">93</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Note on Expected Sample Size Reduction</pre>
+                      <pre class="language-r">#' @return Standard error of log relative treatment effect if `'logged'`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">522</td>
+                    <td class="num">94</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' is true and standard error of the treatment effect if `'logged'`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">523</td>
+                    <td class="num">95</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param width Number of characters to break string into new lines (`\n`).</pre>
+                      <pre class="language-r">#' is false</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">524</td>
+                    <td class="num">96</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">525</td>
+                    <td class="num">97</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return A character string</pre>
+                      <pre class="language-r">#' find_SE_from_CI(CI_lower = 0.55, CI_upper = 0.90, CI_perc = 0.95)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">526</td>
+                    <td class="num">98</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @keywords internal</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">527</td>
+                    <td class="num">99</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ess_footnote_text &lt;- function(width = 0.9 * getOption("width")) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">528</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">100</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  text &lt;- "An ESS reduction up to ~60% is not unexpected based on the 2021 survey of NICE's technology appraisals</pre>
+                      <pre class="language-r">find_SE_from_CI &lt;- function(CI_lower = NULL, CI_upper = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">529</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">101</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">(https://onlinelibrary.wiley.com/doi/full/10.1002/jrsm.1511), whereas a reduction of &gt;75% is less common</pre>
+                      <pre class="language-r">                            CI_perc = 0.95, logged = TRUE) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">530</td>
+                    <td class="num">102</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">and it may be considered suboptimal."</pre>
+                      <pre class="language-r">  if (CI_perc &gt; 1 || CI_perc &lt; 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">531</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">103</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  paste0(strwrap(text, width = width), collapse = "\n")</pre>
+                      <pre class="language-r">    stop("CI_perc has to be between 0 and 1")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">532</td>
+                    <td class="num">104</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/maic_anchored.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">105</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Anchored MAIC for binary and time-to-event endpoint</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">2</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">106</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  if (is.null(CI_lower) || is.null(CI_upper)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">3</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">107</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This is a wrapper function to provide adjusted effect estimates and relevant statistics in anchored case (i.e. there</pre>
+                      <pre class="language-r">    stop("Both CI_lower and CI_upper need to be specified")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">108</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' is a common comparator arm in the internal and external trial).</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">5</td>
+                    <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">6</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">110</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param weights_object an object returned by \code{estimate_weight}</pre>
+                      <pre class="language-r">  if (!is.numeric(CI_lower) || !is.numeric(CI_upper)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">111</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ipd a data frame that meet format requirements in 'Details', individual patient data (IPD) of internal trial</pre>
+                      <pre class="language-r">    stop("Both CI_lower and CI_upper need to be specified")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">112</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param pseudo_ipd a data frame, pseudo IPD from digitized KM curve of external trial (for time-to-event endpoint) or</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">9</td>
+                    <td class="num">113</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   from contingency table (for binary endpoint)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">10</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">114</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_ipd  a string, name of the interested investigation arm in internal trial \code{ipd} (internal IPD)</pre>
+                      <pre class="language-r">  alpha &lt;- 1 - CI_perc</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">11</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">115</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_agd a string, name of the interested investigation arm in external trial \code{pseudo_ipd} (pseudo IPD)</pre>
+                      <pre class="language-r">  se &lt;- ifelse(logged,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">116</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_common a string, name of the common comparator in internal and external trial</pre>
+                      <pre class="language-r">    (log(CI_upper) - log(CI_lower)) / (2 * qnorm(1 - alpha / 2)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">13</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">117</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_var_ipd a string, column name in \code{ipd} that contains the treatment assignment</pre>
+                      <pre class="language-r">    (CI_upper - CI_lower) / (2 * qnorm(1 - alpha / 2))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">14</td>
+                    <td class="num">118</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_var_agd a string, column name in \code{ipd} that contains the treatment assignment</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">15</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">119</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param endpoint_type a string, one out of the following "binary", "tte" (time to event)</pre>
+                      <pre class="language-r">  return(se)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">16</td>
+                    <td class="num">120</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param eff_measure a string, "RD" (risk difference), "OR" (odds ratio), "RR" (relative risk) for a binary endpoint;</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">17</td>
+                    <td class="num">121</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "HR" for a time-to-event endpoint. By default is \code{NULL}, "OR" is used for binary case, otherwise "HR" is used.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">18</td>
+                    <td class="num">122</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param endpoint_name a string, name of time to event endpoint, to be show in the last line of title</pre>
+                      <pre class="language-r">#' Print method for `maicplus_bucher` object</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">19</td>
+                    <td class="num">123</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param time_scale a string, time unit of median survival time, taking a value of 'years', 'months', 'weeks' or</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">20</td>
+                    <td class="num">124</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   'days'. NOTE: it is assumed that values in TIME column of \code{ipd} and \code{pseudo_ipd} is in the unit of days</pre>
+                      <pre class="language-r">#' @param x `maicplus_bucher` object</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">21</td>
+                    <td class="num">125</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param km_conf_type a string, pass to \code{conf.type} of \code{survfit}</pre>
+                      <pre class="language-r">#' @param ci_digits an integer, number of decimal places for point</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">22</td>
+                    <td class="num">126</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param boot_ci_type a string, one of `c("norm","basic", "stud", "perc", "bca")` to select the type of bootstrap</pre>
+                      <pre class="language-r">#' estimate and derived confidence limits</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">23</td>
+                    <td class="num">127</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   confidence interval. See [boot::boot.ci] for more details.</pre>
+                      <pre class="language-r">#' @param pval_digits an integer, number of decimal places to display</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">24</td>
+                    <td class="num">128</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' Z-test p-value</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">25</td>
+                    <td class="num">129</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @details For time-to-event analysis, it is required that input \code{ipd} and \code{pseudo_ipd} to have the following</pre>
+                      <pre class="language-r">#' @param exponentiate whether the treatment effect and confidence</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">130</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   columns. This function is not sensitive to upper or lower case of letters in column names.</pre>
+                      <pre class="language-r">#' interval should be exponentiated. This applies to relative</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">131</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' \itemize{</pre>
+                      <pre class="language-r">#' treatment effects. Default is set to false.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">28</td>
+                    <td class="num">132</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item USUBJID - character, unique subject ID</pre>
+                      <pre class="language-r">#' @param ... not used</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">29</td>
+                    <td class="num">133</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item ARM - character or factor, treatment indicator, column name does not have to be 'ARM'. User specify in</pre>
+                      <pre class="language-r">#' @describeIn bucher Print method for `maicplus_bucher` objects</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">30</td>
+                    <td class="num">134</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'    \code{trt_var_ipd} and \code{trt_var_agd}</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">31</td>
+                    <td class="num">135</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item EVENT - numeric, 1 for censored/death, 0 for otherwise</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">136</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item TIME - numeric column, observation time of the \code{EVENT}; unit in days</pre>
+                      <pre class="language-r">print.maicplus_bucher &lt;- function(x, ci_digits = 2, pval_digits = 3,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">33</td>
+                    <td class="num">137</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">                                  exponentiate = FALSE, ...) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">34</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">138</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  output &lt;- reformat(x, ci_digits, pval_digits,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">35</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">139</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @importFrom survival survfit Surv</pre>
+                      <pre class="language-r">    show_pval = TRUE, exponentiate</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">36</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return A list, contains 'descriptive' and 'inferential'</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">37</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">141</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">  print(output)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">38</td>
+                    <td class="num">142</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">39</td>
+                    <td class="num">143</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">maic_anchored &lt;- function(weights_object,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">40</td>
+                    <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          ipd,</pre>
+                      <pre class="language-r">#' Reformat `maicplus_bucher` alike object</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">41</td>
+                    <td class="num">145</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          pseudo_ipd,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">42</td>
+                    <td class="num">146</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          trt_ipd,</pre>
+                      <pre class="language-r">#' @param x a list, structured like a `maicplus_bucher` object</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">43</td>
+                    <td class="num">147</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          trt_agd,</pre>
+                      <pre class="language-r">#' @param ci_digits an integer, number of decimal places for point</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">44</td>
+                    <td class="num">148</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          trt_common,</pre>
+                      <pre class="language-r">#' estimate and derived confidence limits</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">45</td>
+                    <td class="num">149</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          trt_var_ipd = "ARM",</pre>
+                      <pre class="language-r">#' @param pval_digits an integer, number of decimal places to display</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">46</td>
+                    <td class="num">150</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          trt_var_agd = "ARM",</pre>
+                      <pre class="language-r">#' Z-test p-value</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">47</td>
+                    <td class="num">151</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          endpoint_type = "tte",</pre>
+                      <pre class="language-r">#' @param show_pval a logical value, default is TRUE. If FALSE, p-value will not</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">48</td>
+                    <td class="num">152</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          endpoint_name = "Time to Event Endpoint",</pre>
+                      <pre class="language-r">#' be output as the second element of the character vector</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">49</td>
+                    <td class="num">153</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          eff_measure = c("HR", "OR", "RR", "RD", "Diff"),</pre>
+                      <pre class="language-r">#' @param exponentiate whether the treatment effect and confidence</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">50</td>
+                    <td class="num">154</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          # time to event specific args</pre>
+                      <pre class="language-r">#' interval should be exponentiated. This applies to relative</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">51</td>
+                    <td class="num">155</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          time_scale = "months",</pre>
+                      <pre class="language-r">#' treatment effects. Default is set to false.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">52</td>
+                    <td class="num">156</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          km_conf_type = "log-log",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">53</td>
+                    <td class="num">157</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          boot_ci_type = c("norm", "basic", "stud", "perc", "bca")) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">54</td>
+                    <td class="num">158</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # ==&gt; Initial Setup ------------------------------------------</pre>
+                      <pre class="language-r">reformat &lt;- function(x, ci_digits = 2, pval_digits = 3,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">55</td>
+                    <td class="num">159</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # create the hull for the output from this function</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">56</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  res &lt;- list(</pre>
+                      <pre class="language-r">                     show_pval = TRUE, exponentiate = FALSE) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">57</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">160</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    descriptive = list(),</pre>
+                      <pre class="language-r">  transform_this &lt;- function(x) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">58</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">161</td>
+                    <td class="coverage">18<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    inferential = list()</pre>
+                      <pre class="language-r">    ifelse(exponentiate, exp(x), x)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">59</td>
+                    <td class="num">162</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">60</td>
+                    <td class="num">163</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">61</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">164</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(ipd) &lt;- toupper(names(ipd))</pre>
+                      <pre class="language-r">  a &lt;- format(round(transform_this(x$est), ci_digits),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">62</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">165</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(pseudo_ipd) &lt;- toupper(names(pseudo_ipd))</pre>
+                      <pre class="language-r">    nsmall = ci_digits</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">63</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">166</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  trt_var_ipd &lt;- toupper(trt_var_ipd)</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">64</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  trt_var_agd &lt;- toupper(trt_var_agd)</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">65</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (length(eff_measure) &gt; 1) eff_measure &lt;- NULL</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">66</td>
-                    <td class="coverage">!</td>
+                    <td class="num">167</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(eff_measure)) eff_measure &lt;- list(binary = "OR", tte = "HR")[[endpoint_type]]</pre>
+                      <pre class="language-r">  b &lt;- format(round(transform_this(x$ci_l), ci_digits),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">67</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">168</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    nsmall = ci_digits</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">68</td>
+                    <td class="num">169</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # setup ARM column and precheck</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">69</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (!trt_var_ipd %in% names(ipd)) stop("cannot find arm indicator column trt_var_ipd in ipd")</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">70</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">170</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!trt_var_agd %in% names(pseudo_ipd)) stop("cannot find arm indicator column trt_var_agd in pseudo_ipd")</pre>
+                      <pre class="language-r">  c &lt;- format(round(transform_this(x$ci_u), ci_digits),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">71</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">171</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (trt_var_ipd != "ARM") ipd$ARM &lt;- ipd[[trt_var_ipd]]</pre>
+                      <pre class="language-r">    nsmall = ci_digits</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">72</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">172</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (trt_var_agd != "ARM") pseudo_ipd$ARM &lt;- pseudo_ipd[[trt_var_agd]]</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">73</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">173</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ipd$ARM &lt;- as.character(ipd$ARM) # just to avoid potential error when merging</pre>
+                      <pre class="language-r">  res &lt;- paste0(a, " [", b, "; ", c, "]")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">74</td>
+                    <td class="num">174</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">75</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">175</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # ==&gt; Precheck ------------------------------------------</pre>
+                      <pre class="language-r">  disp_pval &lt;- round(x$pval, pval_digits)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">76</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">176</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pseudo_ipd$ARM &lt;- as.character(pseudo_ipd$ARM) # just to avoid potential error when merging</pre>
+                      <pre class="language-r">  disp_pval &lt;-</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">77</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">177</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!trt_ipd %in% ipd$ARM) stop("trt_ipd does not exist in ipd$ARM")</pre>
+                      <pre class="language-r">    ifelse(disp_pval == 0,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">78</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">178</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!trt_agd %in% pseudo_ipd$ARM) stop("trt_agd does not exist in pseudo_ipd$ARM")</pre>
+                      <pre class="language-r">      paste0("&lt;", 1 / (10^pval_digits)),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">79</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">179</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!trt_common %in% ipd$ARM) stop("trt_common does not exist in ipd$ARM")</pre>
+                      <pre class="language-r">      format(disp_pval, nsmall = pval_digits)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">80</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">180</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!trt_common %in% pseudo_ipd$ARM) stop("trt_common does not exist in pseudo_ipd$ARM")</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">81</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">181</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ipd_arms &lt;- unique(ipd$ARM)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">82</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">182</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pseudo_ipd_arms &lt;- unique(pseudo_ipd$ARM)</pre>
+                      <pre class="language-r">  if (show_pval) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">83</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">183</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!length(ipd_arms) &gt;= 2) {</pre>
+                      <pre class="language-r">    output &lt;- c(res, disp_pval)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">84</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">184</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("In anchored case, there should be at least two arms in ipd, but you have: ", toString(ipd_arms))</pre>
+                      <pre class="language-r">    names(output) &lt;- c("result", "pvalue")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">85</td>
+                    <td class="num">185</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">86</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">186</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!length(pseudo_ipd_arms) &gt;= 2) {</pre>
+                      <pre class="language-r">    output &lt;- res</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">87</td>
+                    <td class="num">187</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("In anchored case, there should be at least two arms in pseudo_ipd, but you have: ", toString(pseudo_ipd_arms))</pre>
+                      <pre class="language-r">    names(output) &lt;- "result"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">88</td>
+                    <td class="num">188</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">89</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">189</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  endpoint_type &lt;- match.arg(endpoint_type, c("binary", "tte"))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">90</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (!"maicplus_estimate_weights" %in% class(weights_object)) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">91</td>
-                    <td class="coverage">!</td>
+                    <td class="num">190</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("weights_object should be an object returned by estimate_weights")</pre>
+                      <pre class="language-r">  output</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">92</td>
+                    <td class="num">191</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">93</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (any(duplicated(ipd$USUBJID))) {</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">94</td>
-                    <td class="coverage">!</td>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/plot_km2.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
+                  <tr class="never">
+                    <td class="num">1</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    warning(</pre>
+                      <pre class="language-r">#' Kaplan-Meier (KM) plot function for anchored and unanchored cases using ggplot</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">95</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">2</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "check your ipd, it has duplicated usubjid, this indicates, ",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">96</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "it might contain multiple endpoints for each subject"</pre>
+                      <pre class="language-r">#' This is wrapper function of \code{basic_kmplot2}.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">97</td>
+                    <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' The argument setting is similar to \code{maic_anchored} and \code{maic_unanchored},</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">98</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' and it is used in those two functions.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">99</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">6</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!all(ipd$USUBJID %in% weights_object$data$USUBJID)) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">100</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">7</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop(</pre>
+                      <pre class="language-r">#' @param weights_object an object returned by \code{estimate_weight}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">101</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">8</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "These patients in ipd cannot be found in weights_object ",</pre>
+                      <pre class="language-r">#' @param tte_ipd a data frame of individual patient data (IPD) of internal trial, contain at least `"USUBJID"`,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">102</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">9</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      toString(setdiff(ipd$USUBJID, weights_object$USUBJID))</pre>
+                      <pre class="language-r">#'   `"EVENT"`, `"TIME"` columns and a column indicating treatment assignment</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">103</td>
+                    <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' @param tte_pseudo_ipd a data frame of pseudo IPD by digitized KM curves of external trial (for time-to-event</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">104</td>
+                    <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#'   endpoint), contain at least `"EVENT"`, `"TIME"`</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">105</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">12</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  time_scale &lt;- match.arg(arg = time_scale, choices = c("days", "weeks", "months", "years"))</pre>
+                      <pre class="language-r">#' @param trt_ipd  a string, name of the interested investigation arm in internal trial \code{dat_igd} (real IPD)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">106</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">13</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (endpoint_type == "binary") { # for binary effect measure</pre>
+                      <pre class="language-r">#' @param trt_agd a string, name of the interested investigation arm in external trial \code{dat_pseudo} (pseudo IPD)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">107</td>
+                    <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param trt_common a string, name of the common comparator in internal and external trial, by default is NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">108</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">15</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (any(!c("USUBJID", "RESPONSE") %in% names(ipd))) stop("ipd should have 'USUBJID', 'RESPONSE' columns at minimum")</pre>
+                      <pre class="language-r">#'   indicating unanchored case</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">109</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">16</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    eff_measure &lt;- match.arg(eff_measure, choices = c("OR", "RD", "RR"), several.ok = FALSE)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">110</td>
-                    <td class="coverage">2<em>x</em></td>
+                      <pre class="language-r">#' @param trt_var_ipd a string, column name in \code{tte_ipd} that contains the treatment assignment</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">17</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else if (endpoint_type == "tte") { # for time to event effect measure</pre>
+                      <pre class="language-r">#' @param trt_var_agd a string, column name in \code{tte_pseudo_ipd} that contains the treatment assignment</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">111</td>
+                    <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param km_conf_type a string, pass to \code{conf.type} of \code{survfit}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">112</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">19</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (!all(c("USUBJID", "TIME", "EVENT", trt_var_ipd) %in% names(ipd))) {</pre>
+                      <pre class="language-r">#' @param km_layout a string, only applicable for unanchored case (\code{trt_common = NULL}), indicated the</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">113</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">20</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("ipd needs to include at least USUBJID, TIME, EVENT, ", toString(trt_var_ipd))</pre>
+                      <pre class="language-r">#'   desired layout of output KM curve.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">114</td>
+                    <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">#' @param time_scale a string, time unit of median survival time, taking a value of 'years', 'months',</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">115</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">22</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (!all(c("TIME", "EVENT", trt_var_agd) %in% names(pseudo_ipd))) {</pre>
+                      <pre class="language-r">#'   weeks' or 'days'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">116</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">23</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      stop("pseudo_ipd needs to include at least TIME, EVENT, ", toString(trt_var_agd))</pre>
+                      <pre class="language-r">#' @param ... other arguments in \code{basic_kmplot2}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">117</td>
+                    <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">118</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">25</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    eff_measure &lt;- match.arg(eff_measure, choices = c("HR"), several.ok = FALSE)</pre>
+                      <pre class="language-r">#' @return In unanchored case, a KM plot with risk set table. In anchored case, depending on \code{km_layout},</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">119</td>
+                    <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#' \itemize{</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">120</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">27</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  boot_ci_type &lt;- match.arg(boot_ci_type)</pre>
+                      <pre class="language-r">#'   \item if "by_trial", 2 by 1 plot, first all KM curves (incl. weighted) in IPD trial, and then KM curves in AgD</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">121</td>
+                    <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # else { # for continuous effect measure</pre>
+                      <pre class="language-r">#'   trial, with risk set table.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">122</td>
+                    <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  #   if (any(!c("USUBJID", "RESPONSE") %in% names(ipd))) {</pre>
+                      <pre class="language-r">#'   \item if "by_arm", 2 by 1 plot, first KM curves of \code{trt_agd} and  \code{trt_ipd} (with and without weights),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">123</td>
+                    <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  #   stop("ipd should have 'USUBJID', 'RESPONSE' columns at minimum")</pre>
+                      <pre class="language-r">#'    and then KM curves of \code{trt_common} in AgD trial and IPD trial (with and without weights). Risk set table is</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">124</td>
+                    <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  #   }</pre>
+                      <pre class="language-r">#'     appended.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">125</td>
+                    <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  #   eff_measure &lt;- match.arg(eff_measure, choices = c("Diff"), several.ok = FALSE)</pre>
+                      <pre class="language-r">#'   \item if "all", 2 by 2 plot, all plots in "by_trial" and "by_arm" without risk set table appended.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">126</td>
+                    <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # }</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">127</td>
+                    <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @example inst/examples/kmplot2_anchored_ex.R</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">128</td>
+                    <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @example inst/examples/kmplot2_unanchored_ex.R</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">129</td>
+                    <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # ==&gt; IPD and AgD data preparation ------------------------------------------</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">130</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">37</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ipd &lt;- ipd[ipd$ARM %in% c(trt_ipd, trt_common), , drop = TRUE]</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">131</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">38</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pseudo_ipd &lt;- pseudo_ipd[pseudo_ipd$ARM %in% c(trt_agd, trt_common), , drop = TRUE]</pre>
+                      <pre class="language-r">kmplot2 &lt;- function(weights_object,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">132</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">39</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ipd$weights &lt;- weights_object$data$weights[match(weights_object$data$USUBJID, ipd$USUBJID)]</pre>
+                      <pre class="language-r">                    tte_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">133</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">40</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pseudo_ipd$weights &lt;- 1</pre>
+                      <pre class="language-r">                    tte_pseudo_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">134</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">41</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!"USUBJID" %in% names(pseudo_ipd)) pseudo_ipd$USUBJID &lt;- paste0("ID", seq_len(nrow(pseudo_ipd)))</pre>
+                      <pre class="language-r">                    trt_ipd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">135</td>
+                    <td class="num">42</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                    trt_agd,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">136</td>
+                    <td class="num">43</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # give warning when individual pts in IPD has no weights</pre>
+                      <pre class="language-r">                    trt_common = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">137</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">44</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (any(is.na(ipd$weights))) {</pre>
+                      <pre class="language-r">                    trt_var_ipd = "ARM",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">138</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">45</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ipd &lt;- ipd[!is.na(ipd$weights), , drop = FALSE]</pre>
+                      <pre class="language-r">                    trt_var_agd = "ARM",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">139</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">46</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    warning(</pre>
+                      <pre class="language-r">                    km_conf_type = "log-log",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">140</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">47</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "These USUBJID in IPD have no weight in weights_object and hence excluded from analysis: ",</pre>
+                      <pre class="language-r">                    km_layout = c("all", "by_trial", "by_arm"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">141</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">48</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      toString(ipd$USUBJID[is.na(ipd$weights)])</pre>
+                      <pre class="language-r">                    time_scale,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">142</td>
+                    <td class="num">49</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">                    ...) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">143</td>
+                    <td class="num">50</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (nrow(ipd) == 0) stop("There are no patients with valid weights in IPD!")</pre>
+                      <pre class="language-r">  if (!requireNamespace("survminer", quietly = TRUE)) stop("survminer package is required for this function")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">144</td>
+                    <td class="num">51</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">145</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">52</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  names(tte_ipd) &lt;- toupper(names(tte_ipd))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">146</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">53</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  outcome_cols &lt;- if (endpoint_type == "tte") c("TIME", "EVENT") else "RESPONSE"</pre>
+                      <pre class="language-r">  names(tte_pseudo_ipd) &lt;- toupper(names(tte_pseudo_ipd))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">147</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">54</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  retain_cols &lt;- c("USUBJID", "ARM", outcome_cols, "weights")</pre>
+                      <pre class="language-r">  trt_var_ipd &lt;- toupper(trt_var_ipd)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">148</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">55</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  trt_var_agd &lt;- toupper(trt_var_agd)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">149</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">56</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ipd &lt;- ipd[, retain_cols, drop = FALSE]</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">150</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">57</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pseudo_ipd &lt;- pseudo_ipd[, retain_cols, drop = FALSE]</pre>
+                      <pre class="language-r">  # pre check</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">151</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">58</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  dat &lt;- rbind(ipd, pseudo_ipd) # only used if apply contrast method</pre>
+                      <pre class="language-r">  if (!"maicplus_estimate_weights" %in% class(weights_object)) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">152</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">59</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ipd$ARM &lt;- factor(ipd$ARM, levels = c(trt_common, trt_ipd))</pre>
+                      <pre class="language-r">    stop("weights_object should be an object returned by estimate_weights")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">153</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">60</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  pseudo_ipd$ARM &lt;- factor(pseudo_ipd$ARM, levels = c(trt_common, trt_agd))</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">154</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">61</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  dat$ARM &lt;- factor(dat$ARM, levels = c(trt_common, trt_agd, trt_ipd))</pre>
+                      <pre class="language-r">  if (!all(c("USUBJID", "TIME", "EVENT", trt_var_ipd) %in% names(tte_ipd))) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">155</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">62</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    stop(paste("tte_ipd needs to include at least USUBJID, TIME, EVENT,", trt_var_ipd))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">156</td>
+                    <td class="num">63</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # ==&gt; Inferential output ------------------------------------------</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">157</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">64</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  result &lt;- if (endpoint_type == "tte") {</pre>
+                      <pre class="language-r">  if (!all(c("TIME", "EVENT", trt_var_agd) %in% names(tte_pseudo_ipd))) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">158</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">65</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    maic_anchored_tte(</pre>
+                      <pre class="language-r">    stop(paste("tte_pseudo_ipd needs to include at least TIME, EVENT,", trt_var_agd))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">159</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">66</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      res, ipd, km_conf_type, pseudo_ipd, time_scale, weights_object, endpoint_name, trt_ipd, trt_agd,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">160</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">67</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      boot_ci_type</pre>
+                      <pre class="language-r">  km_layout &lt;- match.arg(km_layout, choices = c("all", "by_trial", "by_arm"), several.ok = FALSE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">161</td>
+                    <td class="num">68</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">162</td>
+                    <td class="num">69</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">  # preparing data</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">163</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">70</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("Endpoint type ", endpoint_type, " currently unsupported.")</pre>
+                      <pre class="language-r">  is_anchored &lt;- !is.null(trt_common)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">164</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">71</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  tte_ipd &lt;- tte_ipd[tte_ipd[[trt_var_ipd]] %in% c(trt_ipd, trt_common), , drop = FALSE]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">165</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">72</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  tte_pseudo_ipd &lt;- tte_pseudo_ipd[tte_pseudo_ipd[[trt_var_agd]] %in% c(trt_agd, trt_common), , drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">166</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">73</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  result</pre>
+                      <pre class="language-r">  tte_ipd$weights &lt;- weights_object$data$weights[match(weights_object$data$USUBJID, tte_ipd$USUBJID)]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">167</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">74</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  tte_pseudo_ipd$weights &lt;- 1</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">168</td>
+                    <td class="num">75</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">169</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">76</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  tte_ipd$TIME &lt;- get_time_as(tte_ipd$TIME, as = time_scale)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">170</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">77</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># MAIC inference functions by outcome type ------------</pre>
+                      <pre class="language-r">  tte_pseudo_ipd$TIME &lt;- get_time_as(tte_pseudo_ipd$TIME, as = time_scale)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">171</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">78</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  my_survfit &lt;- function(data, weighted = FALSE) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">172</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">79</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">maic_anchored_tte &lt;- function(res,</pre>
+                      <pre class="language-r">    if (weighted) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">173</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">80</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              ipd,</pre>
+                      <pre class="language-r">      survfit(Surv(TIME, EVENT) ~ 1, data = data, conf.type = km_conf_type, weights = data$weights)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">174</td>
+                    <td class="num">81</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              km_conf_type,</pre>
+                      <pre class="language-r">    } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">175</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">82</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              pseudo_ipd,</pre>
+                      <pre class="language-r">      survfit(Surv(TIME, EVENT) ~ 1, data = data, conf.type = km_conf_type)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">176</td>
+                    <td class="num">83</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              time_scale,</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">177</td>
+                    <td class="num">84</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              weights_object,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">178</td>
+                    <td class="num">85</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              endpoint_name,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">179</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">86</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              trt_ipd,</pre>
+                      <pre class="language-r">  if (!is_anchored) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">180</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">87</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              trt_agd,</pre>
+                      <pre class="language-r">    kmlist &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">181</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">88</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              boot_ci_type) {</pre>
+                      <pre class="language-r">      kmobj_B = my_survfit(data = tte_pseudo_ipd),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">182</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">89</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # Analysis table (Cox model) before and after matching, incl Median Survival Time</pre>
+                      <pre class="language-r">      kmobj_A = my_survfit(data = tte_ipd),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">90</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      kmobj_A_adj = my_survfit(data = tte_ipd, weighted = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">183</td>
+                    <td class="num">91</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # derive km w and w/o weights</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">184</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">92</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  kmobj_ipd &lt;- survfit(Surv(TIME, EVENT) ~ ARM, ipd, conf.type = km_conf_type)</pre>
+                      <pre class="language-r">    kmlist_name &lt;- c(trt_agd, trt_ipd, paste0(trt_ipd, " (weighted)"))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">185</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">93</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  kmobj_ipd_adj &lt;- survfit(Surv(TIME, EVENT) ~ ARM, ipd, weights = ipd$weights, conf.type = km_conf_type)</pre>
+                      <pre class="language-r">    basic_kmplot2(kmlist, kmlist_name, ...)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">186</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">94</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  kmobj_agd &lt;- survfit(Surv(TIME, EVENT) ~ ARM, pseudo_ipd, conf.type = km_conf_type)</pre>
+                      <pre class="language-r">  } else if (is_anchored) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">187</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">95</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res$descriptive[["survfit_ipd_before"]] &lt;- survfit_makeup(kmobj_ipd)</pre>
+                      <pre class="language-r">    all_km &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">188</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">96</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res$descriptive[["survfit_ipd_after"]] &lt;- survfit_makeup(kmobj_ipd_adj)</pre>
+                      <pre class="language-r">      kmobj_A = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_ipd, ]),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">189</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">97</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res$descriptive[["survfit_pseudo"]] &lt;- survfit_makeup(kmobj_agd)</pre>
+                      <pre class="language-r">      kmobj_B = my_survfit(data = tte_pseudo_ipd[tte_pseudo_ipd[, trt_var_agd] == trt_agd, ]),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">190</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">98</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # derive median survival time</pre>
+                      <pre class="language-r">      kmobj_A_adj = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_ipd, ], weighted = TRUE),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">191</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">99</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  medSurv_ipd &lt;- medSurv_makeup(kmobj_ipd, legend = "IPD, before matching", time_scale = time_scale)</pre>
+                      <pre class="language-r">      kmobj_C = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_common, ]),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">192</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">100</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  medSurv_ipd_adj &lt;- medSurv_makeup(kmobj_ipd_adj, legend = "IPD, after matching", time_scale = time_scale)</pre>
+                      <pre class="language-r">      kmobj_C_adj = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_common, ], weighted = TRUE),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">193</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">101</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  medSurv_agd &lt;- medSurv_makeup(kmobj_agd, legend = "AgD, external", time_scale = time_scale)</pre>
+                      <pre class="language-r">      kmobj_C_agd = my_survfit(data = tte_pseudo_ipd[tte_pseudo_ipd[, trt_var_agd] == trt_common, ])</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">194</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">102</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  medSurv_out &lt;- rbind(medSurv_ipd, medSurv_ipd_adj, medSurv_agd)</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">195</td>
+                    <td class="num">103</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">196</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">104</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res$inferential[["report_median_surv"]] &lt;- medSurv_out</pre>
+                      <pre class="language-r">    kmlist_combined &lt;- list()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">197</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">105</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    if (km_layout %in% c("by_trial", "all")) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">198</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">106</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # fit PH Cox regression model</pre>
+                      <pre class="language-r">      kmlist_1_2 &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">199</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">107</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  coxobj_ipd &lt;- coxph(Surv(TIME, EVENT) ~ ARM, ipd, robust = TRUE)</pre>
+                      <pre class="language-r">        setNames(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">200</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">108</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  coxobj_ipd_adj &lt;- coxph(Surv(TIME, EVENT) ~ ARM, ipd, weights = weights, robust = TRUE)</pre>
+                      <pre class="language-r">          all_km[c(4, 1, 3, 5)],</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">201</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">109</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  coxobj_agd &lt;- coxph(Surv(TIME, EVENT) ~ ARM, pseudo_ipd, robust = TRUE)</pre>
+                      <pre class="language-r">          c(trt_common, trt_ipd, paste0(trt_ipd, " (weighted)"), paste0(trt_common, " (weighted)"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">202</td>
+                    <td class="num">110</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        ),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">203</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">111</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        setNames(all_km[c(6, 2)], c(trt_common, trt_agd))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">112</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res$inferential[["ipd_coxph_before"]] &lt;- coxobj_ipd</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">204</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">113</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res$inferential[["ipd_coxph_after"]] &lt;- coxobj_ipd_adj</pre>
+                      <pre class="language-r">      names(kmlist_1_2) &lt;- c(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">205</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">114</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_common, ") in the IPD trial"),</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">115</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res$inferential[["agd_coxph"]] &lt;- coxobj_agd</pre>
+                      <pre class="language-r">        paste0("Kaplan-Meier Curves \n(", trt_agd, " vs ", trt_common, ") in the AgD trial")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">206</td>
+                    <td class="num">116</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      )</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">117</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      kmlist_combined &lt;- c(kmlist_combined, kmlist_1_2)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">207</td>
+                    <td class="num">118</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # derive ipd exp arm vs agd exp arm via bucher</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">208</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">119</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res_AC &lt;- as.list(summary(coxobj_ipd_adj)$coef)[c(1, 4)]</pre>
+                      <pre class="language-r">    if (km_layout %in% c("by_arm", "all")) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">209</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">120</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res_BC &lt;- as.list(summary(coxobj_agd)$coef)[c(1, 4)]</pre>
+                      <pre class="language-r">      kmlist_3_4 &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">210</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">121</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(res_AC) &lt;- names(res_BC) &lt;- c("est", "se")</pre>
+                      <pre class="language-r">        setNames(all_km[c(2, 1, 3)], c(trt_agd, trt_ipd, paste0(trt_ipd, " (weighted)"))),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">211</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">122</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res_AB &lt;- bucher(res_AC, res_BC, conf_lv = 0.95)</pre>
+                      <pre class="language-r">        setNames(all_km[c(6, 4, 5)], paste(trt_common, c("(AgD)", "(IPD)", "(IPD,weighted)")))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">212</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">123</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res_AB$est &lt;- exp(res_AB$est)</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">213</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">124</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res_AB$ci_l &lt;- exp(res_AB$ci_l)</pre>
+                      <pre class="language-r">      names(kmlist_3_4) &lt;- c(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">214</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">125</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res_AB$ci_u &lt;- exp(res_AB$ci_u)</pre>
+                      <pre class="language-r">        paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_agd, ")"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">215</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">126</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        paste0("Kaplan-Meier Curves of Common Comparator \n", trt_common, "(IPD vs AgD Trial)")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">216</td>
+                    <td class="num">127</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # get bootstrapped estimates if applicable</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">217</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">128</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res$inferential[["boot_est"]] &lt;- NULL</pre>
+                      <pre class="language-r">      kmlist_combined &lt;- c(kmlist_combined, kmlist_3_4)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">218</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">129</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!is.null(weights_object$boot)) {</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">219</td>
+                    <td class="num">130</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    keep_rows &lt;- setdiff(seq_len(nrow(weights_object$data)), weights_object$rows_with_missing)</pre>
+                      <pre class="language-r">    if (km_layout == "all") {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">220</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">131</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_ipd_id &lt;- weights_object$data[keep_rows, "USUBJID", drop = FALSE]</pre>
+                      <pre class="language-r">      kmlist_combined &lt;- kmlist_combined[c(1, 3, 2, 4)]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">221</td>
+                    <td class="num">132</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    }</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">133</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">222</td>
+                    <td class="num">134</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_ipd &lt;- merge(boot_ipd_id, ipd, by = "USUBJID", all.x = TRUE)</pre>
+                      <pre class="language-r">    splots &lt;- mapply(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">223</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">135</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (nrow(boot_ipd) != nrow(boot_ipd_id)) stop("ipd has multiple observations for some patients")</pre>
+                      <pre class="language-r">      FUN = basic_kmplot2,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">224</td>
+                    <td class="num">136</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_ipd &lt;- boot_ipd[match(boot_ipd$USUBJID, boot_ipd_id$USUBJID), ]</pre>
+                      <pre class="language-r">      kmlist = kmlist_combined,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">225</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">137</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      kmlist_name = lapply(kmlist_combined, names),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">226</td>
+                    <td class="num">138</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stat_fun &lt;- function(data, index, w_obj) {</pre>
+                      <pre class="language-r">      main_title = names(kmlist_combined),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">227</td>
-                    <td class="coverage">6<em>x</em></td>
+                    <td class="num">139</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      r &lt;- dynGet("r", ifnotfound = NA) # Get bootstrap iteration</pre>
+                      <pre class="language-r">      MoreArgs = list(...),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">228</td>
-                    <td class="coverage">6<em>x</em></td>
+                    <td class="num">140</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (!is.na(r)) {</pre>
+                      <pre class="language-r">      SIMPLIFY = FALSE</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">229</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">141</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!all(index == w_obj$boot[, 1, r])) stop("Bootstrap and weight indices don't match")</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">230</td>
-                    <td class="coverage">5<em>x</em></td>
+                    <td class="num">142</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        boot_ipd &lt;- data[w_obj$boot[, 1, r], ]</pre>
+                      <pre class="language-r">    survminer::arrange_ggsurvplots(splots, nrow = 1 + (km_layout == "all"))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">231</td>
-                    <td class="coverage">5<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">143</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        boot_ipd$weights &lt;- w_obj$boot[, 2, r]</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">232</td>
+                    <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">233</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">145</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      boot_coxobj_dat_adj &lt;- coxph(Surv(TIME, EVENT) ~ ARM, boot_ipd, weights = boot_ipd$weights, robust = TRUE)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">234</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">146</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      boot_res_AC &lt;- list(est = coef(boot_coxobj_dat_adj)[1], se = sqrt(vcov(boot_coxobj_dat_adj)[1, 1]))</pre>
+                      <pre class="language-r">#' Basic Kaplan Meier (KM) plot function using ggplot</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">235</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">147</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      boot_res_AB &lt;- bucher(boot_res_AC, res_BC, conf_lv = 0.95)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">236</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">148</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      c(</pre>
+                      <pre class="language-r">#' This function generates a basic KM plot using ggplot.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">237</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">149</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        est_AB = boot_res_AB$est,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">238</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">150</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        var_AB = boot_res_AB$se^2,</pre>
+                      <pre class="language-r">#' @param kmlist a list of \code{survfit} object</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">239</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">151</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        se_AB = boot_res_AB$se,</pre>
+                      <pre class="language-r">#' @param kmlist_name a vector indicating the treatment names of each \code{survfit} object</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">240</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">152</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        est_AC = boot_res_AC$est,</pre>
+                      <pre class="language-r">#' @param endpoint_name a string, name of time to event endpoint, to be show in the</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">241</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">153</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        se_AC = boot_res_AC$se,</pre>
+                      <pre class="language-r">#'   last line of title</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">242</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">154</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        var_AC = boot_res_AC$se^2</pre>
+                      <pre class="language-r">#' @param show_risk_set logical, show risk set table or not, TRUE by default</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">243</td>
+                    <td class="num">155</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' @param main_title a string, main title of the KM plot</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">244</td>
+                    <td class="num">156</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">#' @param break_x_by bin parameter for \code{survminer}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">245</td>
+                    <td class="num">157</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param censor indicator to include censor information</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">246</td>
+                    <td class="num">158</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Revert seed to how it was for weight bootstrap sampling</pre>
+                      <pre class="language-r">#' @param xlim x limit for the x-axis of the plot</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">247</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">159</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    old_seed &lt;- globalenv()$.Random.seed</pre>
+                      <pre class="language-r">#' @param use_colors a character vector of length up to 4, colors to the KM curves,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">248</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">160</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    on.exit(suspendInterrupts(set_random_seed(old_seed)))</pre>
+                      <pre class="language-r">#'   it will be passed to 'col' of \code{lines()}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">249</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">161</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    set_random_seed(weights_object$boot_seed)</pre>
+                      <pre class="language-r">#' @param use_line_types a numeric vector of length up to 4, line type to the KM curves,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">250</td>
+                    <td class="num">162</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   it will be passed to \code{lty} of \code{lines()}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">251</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">163</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    R &lt;- dim(weights_object$boot)[3]</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">252</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">164</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_res &lt;- boot(boot_ipd, stat_fun, R = R, w_obj = weights_object, strata = weights_object$boot_strata)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">253</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">165</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_ci &lt;- boot.ci(boot_res, type = boot_ci_type, w_obj = weights_object)</pre>
+                      <pre class="language-r">basic_kmplot2 &lt;- function(kmlist,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">254</td>
+                    <td class="num">166</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                          kmlist_name,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">255</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">167</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    l_u_index &lt;- switch(boot_ci_type,</pre>
+                      <pre class="language-r">                          endpoint_name = "Time to Event Endpoint",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">256</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">168</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "norm" = list(2, 3, "normal"),</pre>
+                      <pre class="language-r">                          show_risk_set = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">257</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">169</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "basic" = list(4, 5, "basic"),</pre>
+                      <pre class="language-r">                          main_title = "Kaplan-Meier Curves",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">258</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">170</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "stud" = list(4, 5, "student"),</pre>
+                      <pre class="language-r">                          break_x_by = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">259</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">171</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "perc" = list(4, 5, "percent"),</pre>
+                      <pre class="language-r">                          censor = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">260</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">172</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "bca" = list(4, 5, "bca")</pre>
+                      <pre class="language-r">                          xlim = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">261</td>
+                    <td class="num">173</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">                          use_colors = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">262</td>
+                    <td class="num">174</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                          use_line_types = NULL) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">263</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">175</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    res$inferential[["boot_est"]] &lt;- boot_res</pre>
+                      <pre class="language-r">  if (!requireNamespace("survminer", quietly = TRUE)) stop("survminer package is required for this function")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">264</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">176</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    boot_res_AB &lt;- list(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">265</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">177</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      est = exp(boot_res$t0[1]),</pre>
+                      <pre class="language-r">  if (is.null(use_line_types)) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">266</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">178</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      se = NA,</pre>
+                      <pre class="language-r">    use_line_types &lt;- c(1, 1, 2, 2)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">267</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">179</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ci_l = exp(boot_ci[[l_u_index[[3]]]][l_u_index[[1]]]),</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">268</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">180</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ci_u = exp(boot_ci[[l_u_index[[3]]]][l_u_index[[2]]]),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">269</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">181</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pval = NA</pre>
+                      <pre class="language-r">  if (is.null(use_colors)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">270</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">182</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    use_colors &lt;- c("#5450E4", "#00857C", "#6ECEB2", "#7B68EE")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">271</td>
+                    <td class="num">183</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">272</td>
+                    <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">273</td>
+                    <td class="num">185</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # make analysis report table</pre>
+                      <pre class="language-r">  # Produce the Kaplan-Meier plot</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">274</td>
+                    <td class="num">186</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res$inferential[["report_overall_robustCI"]] &lt;- rbind(</pre>
+                      <pre class="language-r">  survminer_plot &lt;- survminer::ggsurvplot(kmlist,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">275</td>
+                    <td class="num">187</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    report_table_tte(coxobj_ipd, medSurv_ipd, tag = paste0("IPD/", endpoint_name)),</pre>
+                      <pre class="language-r">    linetype = use_line_types,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">276</td>
+                    <td class="num">188</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    report_table_tte(coxobj_ipd_adj, medSurv_ipd_adj, tag = paste0("weighted IPD/", endpoint_name)),</pre>
+                      <pre class="language-r">    palette = use_colors,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">277</td>
+                    <td class="num">189</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    report_table_tte(coxobj_agd, medSurv_agd, tag = paste0("Agd/", endpoint_name)),</pre>
+                      <pre class="language-r">    size = 0.2,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">278</td>
+                    <td class="num">190</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    c(</pre>
+                      <pre class="language-r">    combine = TRUE,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">279</td>
+                    <td class="num">191</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      paste0("** adj.", trt_ipd, " vs ", trt_agd),</pre>
+                      <pre class="language-r">    risk.table = show_risk_set,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">280</td>
+                    <td class="num">192</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      rep("-", 4),</pre>
+                      <pre class="language-r">    risk.table.y.text.col = TRUE,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">281</td>
+                    <td class="num">193</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      print(res_AB, pval_digits = 3)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">282</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">283</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">284</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    risk.table.y.text = FALSE,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">285</td>
+                    <td class="num">194</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(res$inferential[["boot_est"]])) {</pre>
+                      <pre class="language-r">    break.x.by = break_x_by,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">286</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    res$inferential[["report_overall_bootCI"]] &lt;- NULL</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">287</td>
-                    <td class="coverage"></td>
+                    <td class="num">195</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">    censor = censor,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">288</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">196</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    temp_boot_res &lt;- boot_res_AB</pre>
+                      <pre class="language-r">    censor.size = 2,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">289</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">197</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    temp_boot_res$ci_l &lt;- boot_res_AB$ci_l</pre>
+                      <pre class="language-r">    xlab = "Time",</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">290</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">198</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    temp_boot_res$ci_u &lt;- boot_res_AB$ci_u</pre>
+                      <pre class="language-r">    ylab = endpoint_name,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">291</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    class(temp_boot_res) &lt;- class(res_AB)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">292</td>
-                    <td class="coverage"></td>
+                    <td class="num">199</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    legend.title = "Treatment",</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">293</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">200</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    res$inferential[["report_overall_bootCI"]] &lt;- rbind(</pre>
+                      <pre class="language-r">    legend = c(0.85, 0.82),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">294</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">201</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      report_table_tte(coxobj_ipd, medSurv_ipd, tag = paste0("IPD/", endpoint_name)),</pre>
+                      <pre class="language-r">    title = paste0(main_title, "\nEndpoint: ", endpoint_name),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">295</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">202</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      report_table_tte(coxobj_ipd_adj, medSurv_ipd_adj, tag = paste0("weighted IPD/", endpoint_name)),</pre>
+                      <pre class="language-r">    legend.labs = kmlist_name,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">296</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">203</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      report_table_tte(coxobj_agd, medSurv_agd, tag = paste0("Agd/", endpoint_name)),</pre>
+                      <pre class="language-r">    tables.theme = survminer::theme_cleantable(),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">297</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">204</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      c(</pre>
+                      <pre class="language-r">    ggtheme = ggplot2::theme_classic(base_size = 10),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">298</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">205</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        paste0("** adj.", trt_ipd, " vs ", trt_agd),</pre>
+                      <pre class="language-r">    fontsize = 3,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">299</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">206</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        rep("-", 4),</pre>
+                      <pre class="language-r">    conf.int = FALSE,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">300</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">        print(temp_boot_res, pval_digits = 3)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">301</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">302</td>
-                    <td class="coverage"></td>
+                    <td class="num">207</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    xlim = xlim</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">303</td>
+                    <td class="num">208</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">304</td>
+                    <td class="num">209</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  res</pre>
+                      <pre class="language-r">  survminer_plot</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">305</td>
+                    <td class="num">210</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
@@ -19346,2256 +21384,2311 @@ <h2>maicplus coverage - 54.75%</h2>
                 </tbody>
               </table>
             </div>
-            <div id="R/bootstrap.R" class="hidden">
+            <div id="R/time-helper.R" class="hidden">
               <table class="table-condensed">
                 <tbody>
                   <tr class="never">
                     <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Bootstrapping weighted hazard ratios to obtain confidence interval</pre>
+                      <pre class="language-r"># Create an environment for settings</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">settings_env &lt;- new.env()</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This function uses \code{\link{boot}} to resample internal IPD data</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' to obtain bootstrapped hazard ratio values which is used to form confidence</pre>
+                      <pre class="language-r">#' Get and Set Time Conversion Factors</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' interval. Note that due to lack of full IPD of covariates in the</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' aggregate data, pseudo IPD will not be bootstrapped.</pre>
+                      <pre class="language-r">#' @param days Factor to divide data time units to get time in days</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @param weeks Factor to divide data time units to get time in weeks</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ipd_centered A data frame containing individual patient data</pre>
+                      <pre class="language-r">#' @param months Factor to divide data time units to get time in months</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   from the internal IPD study. This data frame should have already been</pre>
+                      <pre class="language-r">#' @param years Factor to divide data time units to get time in years</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   centered using [center_ipd] function</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param i Index used to select a sample within \code{\link{boot}}.</pre>
+                      <pre class="language-r">#' @return No value returned. Conversion factors are stored internally and used within functions.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param centered_colnames A character vector giving the names of the covariates to use in matching.</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'  These names must match the column names in internal dataset.</pre>
+                      <pre class="language-r">#' @rdname time_conversion</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param pseudo_ipd A data frame containing pseudo individual patient data</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   from the comparator study needed to derive the relative treatment effect.</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   Pseudo IPD is only used for unanchored case. pseudo_ipd should have time, event,</pre>
+                      <pre class="language-r">#' # Native time format is years</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   and ARM variable with a same name and order as that of ipd_centered</pre>
+                      <pre class="language-r">#' set_time_conversion(days = 1 / 365.25, weeks = 1 / 52.17857, months = 1 / 12, years = 1)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param model Survival model to run to calculate HR with correct time, event, and #'   ARM names</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ref_treat Reference treatment for the survival model</pre>
+                      <pre class="language-r">#' # Native time format is days</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param min_weight A numeric value that defines the minimum weight allowed.</pre>
+                      <pre class="language-r">#' set_time_conversion(days = 1, weeks = 7, months = 365.25 / 12, years = 365.25)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   This value (default 0.0001) will replace weights estimated at 0 in a sample.</pre>
+                      <pre class="language-r">set_time_conversion &lt;- function(days = 1, weeks = 7, months = 365.25 / 12, years = 365.25) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">22</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  settings_env$time_conversion &lt;- c(days = days, weeks = weeks, months = months, years = years)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Unanchored example</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' load(system.file("extdata", "ipd.rda", package = "maicplus", mustWork = TRUE))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' load(system.file("extdata", "agd.rda", package = "maicplus", mustWork = TRUE))</pre>
+                      <pre class="language-r">#' @param factor Time factor to get.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ipd_centered &lt;- center_ipd(ipd = ipd, agd = agd)</pre>
+                      <pre class="language-r">#' @rdname time_conversion</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' pseudo_ipd &lt;- read.csv(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   system.file("extdata", "psuedo_IPD.csv", package = "maicplus", mustWork = TRUE)</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">#' # Get time scale factors:</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' pseudo_ipd$ARM &lt;- "B" # Need to specify ARM for pseudo ipd</pre>
+                      <pre class="language-r">#' get_time_conversion("years")</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' get_time_conversion("weeks")</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Need to ensure pseudo_ipd and ipd_matched have same names</pre>
+                      <pre class="language-r">get_time_conversion &lt;- function(factor = c("days", "weeks", "months", "years")) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">35</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">20<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' colnames(pseudo_ipd) &lt;- c("TIME", "EVENT", "ARM")</pre>
+                      <pre class="language-r">  factor &lt;- match.arg(factor, several.ok = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">36</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">20<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' \dontrun{</pre>
+                      <pre class="language-r">  if (!exists("time_conversion", settings_env)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">37</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' HR_bootstraps &lt;- boot(</pre>
+                      <pre class="language-r">    warning("No time conversion factors previously set. Setting defaults.")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">38</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data = ipd_centered,</pre>
+                      <pre class="language-r">    set_time_conversion()</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   statistic = bootstrap_HR,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">40</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">20<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   centered_colnames = centered_colnames,</pre>
+                      <pre class="language-r">  settings_env$time_conversion[factor]</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   pseudo_ipd = pseudo_ipd,</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">42</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   model = Surv(TIME, EVENT == 1) ~ ARM,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">43</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   ref_treat = "B",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">44</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   R = 1000</pre>
+                      <pre class="language-r">#' Convert Time Values Using Scaling Factors</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">45</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">46</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#' @param times Numeric time values</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return The HR bootstraps</pre>
+                      <pre class="language-r">#' @param as A time scale to convert to</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">48</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">49</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @return Returns a numeric vector calculated from `times / get_time_conversion(factor = as)`</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">50</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">bootstrap_HR &lt;- function(ipd_centered, i, centered_colnames,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">51</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         pseudo_ipd = NULL, model,</pre>
+                      <pre class="language-r">get_time_as &lt;- function(times, as = c("days", "weeks", "months", "years")) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">52</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         min_weight = 0.0001, ref_treat = NULL) {</pre>
+                      <pre class="language-r">  if (!is.numeric(times)) stop("times arguments must be numeric")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">53</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">20<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # Resamples the centered internal IPD data</pre>
+                      <pre class="language-r">  as &lt;- match.arg(as)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">54</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">20<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  bootstrap_data &lt;- ipd_centered[i, ]</pre>
+                      <pre class="language-r">  times / get_time_conversion(as)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">55</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/binary-helper.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
                   <tr class="never">
-                    <td class="num">56</td>
+                    <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # Estimates weights</pre>
+                      <pre class="language-r">#' Create pseudo IPD given aggregated binary data</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">57</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">2</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  weighted_data &lt;- estimate_weights(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">58</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    data = bootstrap_data,</pre>
+                      <pre class="language-r">#' @param binary_agd a data.frame that take different formats depending on \code{format}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">59</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">4</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    centered_colnames = centered_colnames</pre>
+                      <pre class="language-r">#' @param format a string, "stacked" or "unstacked"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">60</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">61</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @return a data.frame of pseudo binary IPD, with columns USUBJID, ARM, RESPONSE</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">62</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">7</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ipd_matched &lt;- weighted_data$data</pre>
+                      <pre class="language-r">#' @example inst/examples/get_pseudo_ipd_binary_ex.R</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">63</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">8</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (length(unique(ipd_matched$ARM)) == 2) { # this is the anchored case</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">64</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">9</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    combined_data &lt;- ipd_matched</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">65</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">10</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else if (length(unique(ipd_matched$ARM)) == 1) { # this is the unanchored case</pre>
+                      <pre class="language-r">get_pseudo_ipd_binary &lt;- function(binary_agd, format = c("stacked", "unstacked")) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">66</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">11</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (is.null(pseudo_ipd)) stop("For unanchored case pseudo_ipd needs to be specified")</pre>
+                      <pre class="language-r">  # pre check</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">12</td>
+                    <td class="coverage">4<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (format == "stacked") {</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">13</td>
+                    <td class="coverage">3<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    if (!is.data.frame(binary_agd)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">67</td>
+                    <td class="num">14</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (is.null(pseudo_ipd$ARM)) stop("external data should have an ARM column")</pre>
+                      <pre class="language-r">      stop("stacked binary_agd should be data.frame with columns 'ARM', 'RESPONSE', 'COUNT'")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">68</td>
+                    <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">69</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">16</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Assign weight of 1 for pseudo_ipd if it not defined already</pre>
+                      <pre class="language-r">    names(binary_agd) &lt;- toupper(names(binary_agd))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">70</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">17</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pseudo_ipd$weights &lt;- 1</pre>
+                      <pre class="language-r">    if (!all(c("ARM", "RESPONSE", "COUNT") %in% names(binary_agd))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">71</td>
+                    <td class="num">18</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    combined_data &lt;- rbind(</pre>
+                      <pre class="language-r">      stop("stacked binary_agd should be data.frame with columns 'ARM', 'Response', 'Count'")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">72</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">19</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ipd_matched[, colnames(pseudo_ipd)],</pre>
+                      <pre class="language-r">    }</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">20</td>
+                    <td class="coverage">3<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    if (!is.logical(binary_agd$RESPONSE) &amp;&amp; !all(toupper(binary_agd$RESPONSE) %in% c("YES", "NO"))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">73</td>
+                    <td class="num">21</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pseudo_ipd</pre>
+                      <pre class="language-r">      stop("'RESPONSE' column in stacked binary_agd should be either logical vector or character vector of 'Yes'/'No'")</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">22</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    }</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">23</td>
+                    <td class="coverage">3<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    if (nrow(binary_agd) %% 2 != 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">74</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">24</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">      stop("nrow(binary_agd) is not even number, you may miss to provide 1 level of binary response to certain arm")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">75</td>
+                    <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">76</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">26</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("ipd_matched ARM should have 1 or 2 treatments")</pre>
+                      <pre class="language-r">  } else if (format == "unstacked") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">77</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">27</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    if (!(is.data.frame(binary_agd) || is.matrix(binary_agd))) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">78</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">28</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      stop("unstacked binary_agd should be either a 1x2 or 2x2 data frame or matrix")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">79</td>
+                    <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # set the base treatment</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">80</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">30</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(ref_treat)) stop("Need to specify a value for ref_treat")</pre>
+                      <pre class="language-r">    if (ncol(binary_agd) != 2 || !nrow(binary_agd) %in% c(1, 2)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">81</td>
+                    <td class="num">31</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  combined_data$ARM &lt;- stats::relevel(as.factor(combined_data$ARM), ref = ref_treat)</pre>
+                      <pre class="language-r">      stop("unstacked binary_agd should be either a 1x2 or 2x2 data frame or matrix")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">82</td>
+                    <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">83</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">33</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # set weights that are below min_weight to min_weight to avoid issues with 0 values</pre>
+                      <pre class="language-r">    bin_res &lt;- toupper(colnames(binary_agd))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">84</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">34</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  combined_data$weights &lt;- ifelse(combined_data$weights &lt; min_weight, min_weight, combined_data$weights)</pre>
+                      <pre class="language-r">    bin_res &lt;- sort(bin_res)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">85</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">35</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  cox_model &lt;- survival::coxph(model, data = combined_data, weights = weights, robust = TRUE)</pre>
+                      <pre class="language-r">    if (!(identical(bin_res, c("FALSE", "TRUE")) || identical(bin_res, c("NO", "YES")))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">86</td>
+                    <td class="num">36</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  HR &lt;- exp(cox_model$coefficients)</pre>
+                      <pre class="language-r">      stop("column names of unstacked binary_agd should be either TRUE/FALSE or Yes/No")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">87</td>
+                    <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">88</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">38</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  return(HR)</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">89</td>
+                    <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/utils.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># Restore the RNG back to a previous state using the global .Random.seed</pre>
+                      <pre class="language-r">  # pre process binary_agd, depending on format</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">2</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">41</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">set_random_seed &lt;- function(old_seed) {</pre>
+                      <pre class="language-r">  use_binary_agd &lt;- switch(format,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">3</td>
-                    <td class="coverage">12<em>x</em></td>
+                    <td class="num">42</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(old_seed)) {</pre>
+                      <pre class="language-r">    "stacked" = {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">4</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">43</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    rm(".Random.seed", envir = globalenv(), inherits = FALSE)</pre>
+                      <pre class="language-r">      names(binary_agd) &lt;- toupper(names(binary_agd))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">5</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">44</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">      if (!is.logical(binary_agd$RESPONSE)) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">6</td>
-                    <td class="coverage">12<em>x</em></td>
+                    <td class="num">45</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assign(".Random.seed", value = old_seed, envir = globalenv(), inherits = FALSE)</pre>
+                      <pre class="language-r">        binary_agd$RESPONSE &lt;- toupper(binary_agd$RESPONSE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">46</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">        binary_agd$RESPONSE &lt;- binary_agd$RESPONSE == "YES"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">9</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">48</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      binary_agd</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">10</td>
+                    <td class="num">49</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">construct_boot_data &lt;- function(weighted_data, i = 1) {</pre>
+                      <pre class="language-r">    },</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">11</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">50</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(weighted_data$boot)) stop("Must contain bootstrap results from estimate_weights()")</pre>
+                      <pre class="language-r">    "unstacked" = {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">12</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">51</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  i &lt;- as.integer(i)</pre>
+                      <pre class="language-r">      trt_names &lt;- rownames(binary_agd)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">13</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">52</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  R &lt;- dim(weighted_data$boot)[3]</pre>
+                      <pre class="language-r">      bin_res &lt;- toupper(colnames(binary_agd))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">14</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">53</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (i &lt; 1 || i &gt; R) stop("i must be integer between 1 and ", R)</pre>
+                      <pre class="language-r">      if ("YES" %in% bin_res) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">15</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">54</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        bin_res &lt;- ifelse(bin_res == "YES", "TRUE", "FALSE")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">16</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">55</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  boot_data &lt;- weighted_data$boot[, , i]</pre>
+                      <pre class="language-r">        colnames(binary_agd) &lt;- bin_res</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">17</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">56</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  weighted_data$data &lt;- weighted_data$data[boot_data[, 1], ]</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">18</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">57</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  weighted_data$data$weights &lt;- boot_data[, 2]</pre>
+                      <pre class="language-r">      tmpout &lt;- utils::stack(binary_agd)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">19</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">58</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  weighted_data$data$scaled_weights &lt;- boot_data[, 2] / sum(boot_data[, 2])</pre>
+                      <pre class="language-r">      tmpout &lt;- cbind(ARM = rep(trt_names, each = 2), tmpout)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">20</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">59</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  weighted_data</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">21</td>
-                    <td class="coverage"></td>
+                      <pre class="language-r">      names(tmpout) &lt;- c("ARM", "COUNT", "RESPONSE")</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">60</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      rownames(tmpout) &lt;- NULL</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/plot_km2.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
-                  <tr class="never">
-                    <td class="num">1</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">61</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Kaplan-Meier (KM) plot function for anchored and unanchored cases using ggplot</pre>
+                      <pre class="language-r">      tmpout$RESPONSE &lt;- as.logical(tmpout$RESPONSE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">2</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">62</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      tmpout</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">63</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This is wrapper function of \code{basic_kmplot2}.</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">64</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' The argument setting is similar to \code{maic_anchored} and \code{maic_unanchored},</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">5</td>
+                    <td class="num">65</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' and it is used in those two functions.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">6</td>
+                    <td class="num">66</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  # create pseudo binary IPD</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">67</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param weights_object an object returned by \code{estimate_weight}</pre>
+                      <pre class="language-r">  use_binary_agd$ARM &lt;- factor(use_binary_agd$ARM, levels = unique(use_binary_agd$ARM))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">8</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">68</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param tte_ipd a data frame of individual patient data (IPD) of internal trial, contain at least `"USUBJID"`,</pre>
+                      <pre class="language-r">  n_per_arm &lt;- tapply(use_binary_agd$COUNT, use_binary_agd$ARM, sum)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">9</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">69</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   `"EVENT"`, `"TIME"` columns and a column indicating treatment assignment</pre>
+                      <pre class="language-r">  n_yes_per_arm &lt;- use_binary_agd$COUNT[use_binary_agd$RESPONSE] # use_binary_agd is already ordered as per factor ARM</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">10</td>
+                    <td class="num">70</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param tte_pseudo_ipd a data frame of pseudo IPD by digitized KM curves of external trial (for time-to-event</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">11</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">71</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   endpoint), contain at least `"EVENT"`, `"TIME"`</pre>
+                      <pre class="language-r">  tmpipd &lt;- data.frame(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">72</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_ipd  a string, name of the interested investigation arm in internal trial \code{dat_igd} (real IPD)</pre>
+                      <pre class="language-r">    USUBJID = NA,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">13</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">73</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_agd a string, name of the interested investigation arm in external trial \code{dat_pseudo} (pseudo IPD)</pre>
+                      <pre class="language-r">    ARM = unlist(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">14</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">74</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_common a string, name of the common comparator in internal and external trial, by default is NULL,</pre>
+                      <pre class="language-r">      mapply(rep, x = levels(use_binary_agd$ARM), each = n_per_arm, SIMPLIFY = FALSE, USE.NAMES = FALSE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">15</td>
+                    <td class="num">75</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   indicating unanchored case</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">16</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">76</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_var_ipd a string, column name in \code{tte_ipd} that contains the treatment assignment</pre>
+                      <pre class="language-r">    RESPONSE = unlist(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">17</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">77</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param trt_var_agd a string, column name in \code{tte_pseudo_ipd} that contains the treatment assignment</pre>
+                      <pre class="language-r">      lapply(seq_along(n_per_arm), function(ii) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">18</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">78</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param km_conf_type a string, pass to \code{conf.type} of \code{survfit}</pre>
+                      <pre class="language-r">        c(rep(TRUE, n_yes_per_arm[ii]), rep(FALSE, n_per_arm[ii] - n_yes_per_arm[ii]))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">19</td>
+                    <td class="num">79</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param km_layout a string, only applicable for unanchored case (\code{trt_common = NULL}), indicated the</pre>
+                      <pre class="language-r">      })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">20</td>
+                    <td class="num">80</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   desired layout of output KM curve.</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">21</td>
+                    <td class="num">81</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param time_scale a string, time unit of median survival time, taking a value of 'years', 'months',</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">22</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">82</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   weeks' or 'days'</pre>
+                      <pre class="language-r">  tmpipd$USUBJID &lt;- paste0("pseudo_binary_subj_", seq_len(nrow(tmpipd)))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">23</td>
+                    <td class="num">83</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ... other arguments in \code{basic_kmplot2}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">24</td>
+                    <td class="num">84</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  # output</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">25</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">85</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return In unanchored case, a KM plot with risk set table. In anchored case, depending on \code{km_layout},</pre>
+                      <pre class="language-r">  tmpipd</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">86</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' \itemize{</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/data_generation.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item if "by_trial", 2 by 1 plot, first all KM curves (incl. weighted) in IPD trial, and then KM curves in AgD</pre>
+                      <pre class="language-r">#' Generate time-to-event data</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">28</td>
+                    <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   trial, with risk set table.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">29</td>
+                    <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item if "by_arm", 2 by 1 plot, first KM curves of \code{trt_agd} and  \code{trt_ipd} (with and without weights),</pre>
+                      <pre class="language-r">#' Function generates time-to-event data. We follow the data-generating mechanism from</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">30</td>
+                    <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'    and then KM curves of \code{trt_common} in AgD trial and IPD trial (with and without weights). Risk set table is</pre>
+                      <pre class="language-r">#' Bender et al. and Remiro-Azocar et al. 2021 to simulate Weibull-distributed survival times</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">31</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     appended.</pre>
+                      <pre class="language-r">#' under a proportional hazards parameterization. As per Remiro-Azocar et al, we set the</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   \item if "all", 2 by 2 plot, all plots in "by_trial" and "by_arm" without risk set table appended.</pre>
+                      <pre class="language-r">#' default scale parameter (lambda) to 8.5 and shape parameter (nu) to 1.3 to reflect frequently</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">33</td>
+                    <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#' observed mortality trends in metastatic cancer patients. Censoring times are generated from</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">34</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @example inst/examples/kmplot2_anchored_ex.R</pre>
+                      <pre class="language-r">#' exponential distribution where the rate parameter is 0.96 is selected to achieve a censoring rate</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">35</td>
+                    <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @example inst/examples/kmplot2_unanchored_ex.R</pre>
+                      <pre class="language-r">#' of 35% under the active treatment at baseline (with the values of the covariates set to zero).</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">36</td>
+                    <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">37</td>
+                    <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @param N sample size</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">38</td>
+                    <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">kmplot2 &lt;- function(weights_object,</pre>
+                      <pre class="language-r">#' @param ncov number of covariates to generate</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">39</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    tte_ipd,</pre>
+                      <pre class="language-r">#' @param lambda scale parameter in baseline hazard function</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">40</td>
+                    <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    tte_pseudo_ipd,</pre>
+                      <pre class="language-r">#' @param nu shape parameter in baseline hazard function</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">41</td>
+                    <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    trt_ipd,</pre>
+                      <pre class="language-r">#' @param censor_rate rate parameter of the exponential distribution of censoring times</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">42</td>
+                    <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    trt_agd,</pre>
+                      <pre class="language-r">#' @param cor correlation between covariates</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">43</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    trt_common = NULL,</pre>
+                      <pre class="language-r">#' @param marginal_mean marginal mean of covariates</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">44</td>
+                    <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    trt_var_ipd = "ARM",</pre>
+                      <pre class="language-r">#' @param marginal_sd marginal standard deviation of covariates</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">45</td>
+                    <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    trt_var_agd = "ARM",</pre>
+                      <pre class="language-r">#' @param beta vector of coefficients for prognostic factors. Defaults is `-log(0.67)` for all covariates.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">46</td>
+                    <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    km_conf_type = "log-log",</pre>
+                      <pre class="language-r">#' @param gamma vector of coefficients for effect modifiers. Default is `0` for half of the covariates and</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">47</td>
+                    <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    km_layout = c("all", "by_trial", "by_arm"),</pre>
+                      <pre class="language-r">#'  `-log(0.67)` for the others.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">48</td>
+                    <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    time_scale,</pre>
+                      <pre class="language-r">#' @param d0 coefficient for the treatment effect for patients with `treat = 0`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">49</td>
+                    <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    ...) {</pre>
+                      <pre class="language-r">#' @param seed seed used for simulation reproducibility</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">50</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">24</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!requireNamespace("survminer", quietly = TRUE)) stop("survminer package is required for this function")</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">51</td>
+                    <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @return data.frame with survival time, censor (event) status, treatment indicator, and covariates</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">52</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">26</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(tte_ipd) &lt;- toupper(names(tte_ipd))</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">53</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">27</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  names(tte_pseudo_ipd) &lt;- toupper(names(tte_pseudo_ipd))</pre>
+                      <pre class="language-r">#' @references Remiro-Azocar et al. 2021</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">54</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">28</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  trt_var_ipd &lt;- toupper(trt_var_ipd)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">55</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">29</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  trt_var_agd &lt;- toupper(trt_var_agd)</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">56</td>
+                    <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">57</td>
+                    <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # pre check</pre>
+                      <pre class="language-r">generate_survival_data &lt;- function(N = 150, ncov = 4, lambda = 8.5, nu = 1.3, censor_rate = 0.96,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">58</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">32</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!"maicplus_estimate_weights" %in% class(weights_object)) {</pre>
+                      <pre class="language-r">                                   cor = 0.35, marginal_mean = 0.6, marginal_sd = 0.2,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">59</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">33</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop("weights_object should be an object returned by estimate_weights")</pre>
+                      <pre class="language-r">                                   beta = rep(-log(0.67), ncov),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">60</td>
+                    <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">                                   gamma = sort(rep(c(0, -log(0.67)), length = ncov)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">61</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">35</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!all(c("USUBJID", "TIME", "EVENT", trt_var_ipd) %in% names(tte_ipd))) {</pre>
+                      <pre class="language-r">                                   d0 = log(0.25), seed = 1) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">62</td>
+                    <td class="num">36</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop(paste("tte_ipd needs to include at least USUBJID, TIME, EVENT,", trt_var_ipd))</pre>
+                      <pre class="language-r">  set.seed(seed)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">63</td>
+                    <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">64</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">38</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!all(c("TIME", "EVENT", trt_var_agd) %in% names(tte_pseudo_ipd))) {</pre>
+                      <pre class="language-r">  # if beta and gamma is not specified, give it default values</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">65</td>
+                    <td class="num">39</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    stop(paste("tte_pseudo_ipd needs to include at least TIME, EVENT,", trt_var_agd))</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">66</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  if (is.null(beta)) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">67</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">40</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  km_layout &lt;- match.arg(km_layout, choices = c("all", "by_trial", "by_arm"), several.ok = FALSE)</pre>
+                      <pre class="language-r">    beta &lt;- rep(-log(0.67), ncov)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">68</td>
+                    <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">69</td>
+                    <td class="num">42</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # preparing data</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">70</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  is_anchored &lt;- !is.null(trt_common)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">71</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">43</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_ipd &lt;- tte_ipd[tte_ipd[[trt_var_ipd]] %in% c(trt_ipd, trt_common), , drop = FALSE]</pre>
+                      <pre class="language-r">  if (is.null(gamma)) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">72</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">44</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_pseudo_ipd &lt;- tte_pseudo_ipd[tte_pseudo_ipd[[trt_var_agd]] %in% c(trt_agd, trt_common), , drop = FALSE]</pre>
+                      <pre class="language-r">    gamma &lt;- rep(-log(0.67), ncov)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">73</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">45</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_ipd$weights &lt;- weights_object$data$weights[match(weights_object$data$USUBJID, tte_ipd$USUBJID)]</pre>
+                      <pre class="language-r">    gamma[1:round(ncov / 2)] &lt;- 0</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">74</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">46</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tte_pseudo_ipd$weights &lt;- 1</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">75</td>
+                    <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">76</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  tte_ipd$TIME &lt;- get_time_as(tte_ipd$TIME, as = time_scale)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">77</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  tte_pseudo_ipd$TIME &lt;- get_time_as(tte_pseudo_ipd$TIME, as = time_scale)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">78</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  my_survfit &lt;- function(data, weighted = FALSE) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">79</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">48</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (weighted) {</pre>
+                      <pre class="language-r">  # generate ncov covariates (X) using a multivariate normal</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">80</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">49</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      survfit(Surv(TIME, EVENT) ~ 1, data = data, conf.type = km_conf_type, weights = data$weights)</pre>
+                      <pre class="language-r">  sigma &lt;- matrix(cor, nrow = ncov, ncol = ncov)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">81</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">50</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    } else {</pre>
+                      <pre class="language-r">  diag(sigma) &lt;- 1</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">82</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">51</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      survfit(Surv(TIME, EVENT) ~ 1, data = data, conf.type = km_conf_type)</pre>
+                      <pre class="language-r">  sigma &lt;- sigma * marginal_sd^2</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">83</td>
+                    <td class="num">52</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">84</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">53</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  covariates &lt;- MASS::mvrnorm(N, mu = rep(marginal_mean, ncov), Sigma = sigma)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">85</td>
+                    <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">86</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (!is_anchored) {</pre>
-                    </td>
-                  </tr>
                   <tr class="missed">
-                    <td class="num">87</td>
+                    <td class="num">55</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmlist &lt;- list(</pre>
+                      <pre class="language-r">  treat &lt;- sample(x = c(0, 1), size = N, replace = TRUE, prob = c(0.5, 0.5))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">56</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">88</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">57</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmobj_B = my_survfit(data = tte_pseudo_ipd),</pre>
+                      <pre class="language-r">  # linear predictor</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">89</td>
+                    <td class="num">58</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmobj_A = my_survfit(data = tte_ipd),</pre>
+                      <pre class="language-r">  lp &lt;- covariates %*% beta + covariates %*% gamma * treat + d0 * treat</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">90</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">59</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmobj_A_adj = my_survfit(data = tte_ipd, weighted = TRUE)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">91</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  # Weibull latent event times</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">92</td>
+                    <td class="num">61</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmlist_name &lt;- c(trt_agd, trt_ipd, paste0(trt_ipd, " (weighted)"))</pre>
+                      <pre class="language-r">  u &lt;- runif(n = N)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">93</td>
+                    <td class="num">62</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    basic_kmplot2(kmlist, kmlist_name, ...)</pre>
+                      <pre class="language-r">  latent_time &lt;- (-log(u) / (lambda * exp(lp)))^(1 / nu)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">94</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">63</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else if (is_anchored) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">95</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">64</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    all_km &lt;- list(</pre>
+                      <pre class="language-r">  # exponential censoring times</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">96</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">65</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmobj_A = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_ipd, ]),</pre>
+                      <pre class="language-r">  censor_time &lt;- rexp(n = N, rate = censor_rate)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">97</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">66</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmobj_B = my_survfit(data = tte_pseudo_ipd[tte_pseudo_ipd[, trt_var_agd] == trt_agd, ]),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">98</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">67</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmobj_A_adj = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_ipd, ], weighted = TRUE),</pre>
+                      <pre class="language-r">  # follow-up times and event indicators</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">99</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">68</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmobj_C = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_common, ]),</pre>
+                      <pre class="language-r">  time &lt;- pmin(latent_time, censor_time)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">100</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">69</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmobj_C_adj = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_common, ], weighted = TRUE),</pre>
+                      <pre class="language-r">  event &lt;- as.numeric(latent_time &lt;= censor_time)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">101</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">70</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmobj_C_agd = my_survfit(data = tte_pseudo_ipd[tte_pseudo_ipd[, trt_var_agd] == trt_common, ])</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">102</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">71</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  colnames(covariates) &lt;- paste0("x", seq_len(ncov))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">103</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">72</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  survival_data &lt;- data.frame(USUBJID = seq_len(N), time = time, event = event, treat = treat, x = covariates)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">104</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">73</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    kmlist_combined &lt;- list()</pre>
+                      <pre class="language-r">  return(survival_data)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">105</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">74</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (km_layout %in% c("by_trial", "all")) {</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">106</td>
-                    <td class="coverage">1<em>x</em></td>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/reporting.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
+                  <tr class="never">
+                    <td class="num">1</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmlist_1_2 &lt;- list(</pre>
+                      <pre class="language-r">#' helper function: sort out a nice report table to summarize survival analysis results</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">107</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">2</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        setNames(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">108</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          all_km[c(4, 1, 3, 5)],</pre>
+                      <pre class="language-r">#' @param coxobj returned object from \code{\link[survival]{coxph}}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">109</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">4</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          c(trt_common, trt_ipd, paste0(trt_ipd, " (weighted)"), paste0(trt_common, " (weighted)"))</pre>
+                      <pre class="language-r">#' @param medSurvobj returned object from \code{\link{medSurv_makeup}}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">110</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ),</pre>
+                      <pre class="language-r">#' @param tag a string, by default NULL, if specified, an extra 1st column is created in the output</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">111</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">6</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        setNames(all_km[c(6, 2)], c(trt_common, trt_agd))</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">112</td>
+                    <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' @return a data frame with sample size, incidence rate, median survival time with 95% CI, hazard ratio estimate with</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">113</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">8</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      names(kmlist_1_2) &lt;- c(</pre>
+                      <pre class="language-r">#' 95% CI and Wald test of hazard ratio</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">114</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">9</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_common, ") in the IPD trial"),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">115</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">10</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        paste0("Kaplan-Meier Curves \n(", trt_agd, " vs ", trt_common, ") in the AgD trial")</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">116</td>
+                    <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">117</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">12</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmlist_combined &lt;- c(kmlist_combined, kmlist_1_2)</pre>
+                      <pre class="language-r">report_table_tte &lt;- function(coxobj, medSurvobj, tag = NULL) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">118</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">  # descriptive part</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">119</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">14</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (km_layout %in% c("by_arm", "all")) {</pre>
+                      <pre class="language-r">  N &lt;- medSurvobj$n.max</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">120</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">15</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmlist_3_4 &lt;- list(</pre>
+                      <pre class="language-r">  N.EVNT &lt;- medSurvobj$events</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">121</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">16</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        setNames(all_km[c(2, 1, 3)], c(trt_agd, trt_ipd, paste0(trt_ipd, " (weighted)"))),</pre>
+                      <pre class="language-r">  N.EVNT.PERC &lt;- round(N.EVNT * 100 / N, 1)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">122</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">17</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        setNames(all_km[c(6, 4, 5)], paste(trt_common, c("(AgD)", "(IPD)", "(IPD,weighted)")))</pre>
+                      <pre class="language-r">  N &lt;- round(N, 1) # not necessary integer</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">123</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">18</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">  N.EVNT &lt;- round(N.EVNT, 1) # not necessary integer</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">124</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">19</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      names(kmlist_3_4) &lt;- c(</pre>
+                      <pre class="language-r">  meds_report &lt;- format(round(medSurvobj[, c("median", "0.95LCL", "0.95UCL")], 1), nsmall = 1)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">125</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">20</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_agd, ")"),</pre>
+                      <pre class="language-r">  meds_report &lt;- apply(meds_report, 1, function(xx) paste0(xx[1], "[", xx[2], ";", xx[3], "]"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">126</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">21</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        paste0("Kaplan-Meier Curves of Common Comparator \n", trt_common, "(IPD vs AgD Trial)")</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">127</td>
+                    <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">  # inferential part</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">128</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">23</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmlist_combined &lt;- c(kmlist_combined, kmlist_3_4)</pre>
+                      <pre class="language-r">  hr_res &lt;- format(round(summary(coxobj)$conf.int[-2], 2), nsmall = 2)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">129</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">24</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">  hr_res &lt;- paste0(hr_res[1], "[", hr_res[2], ";", hr_res[3], "]")</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">130</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">25</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (km_layout == "all") {</pre>
+                      <pre class="language-r">  hr_pval &lt;- format(round(summary(coxobj)$waldtest[3], 3), nsmall = 3)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">131</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">26</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmlist_combined &lt;- kmlist_combined[c(1, 3, 2, 4)]</pre>
+                      <pre class="language-r">  if (hr_pval == "0.000") hr_pval &lt;- "&lt;0.001"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">132</td>
+                    <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">133</td>
+                    <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # assemble the table</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">134</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">29</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    splots &lt;- mapply(</pre>
+                      <pre class="language-r">  desc_res &lt;- cbind(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">135</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">30</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      FUN = basic_kmplot2,</pre>
+                      <pre class="language-r">    medSurvobj[, "treatment", drop = FALSE],</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">136</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">31</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmlist = kmlist_combined,</pre>
+                      <pre class="language-r">    data.frame(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">137</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">32</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      kmlist_name = lapply(kmlist_combined, names),</pre>
+                      <pre class="language-r">      "N" = N,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">138</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">33</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      main_title = names(kmlist_combined),</pre>
+                      <pre class="language-r">      "n.events(%)" = paste0(N.EVNT, "(", format(N.EVNT.PERC, nsmall = 1), ")"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">139</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">34</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      MoreArgs = list(...),</pre>
+                      <pre class="language-r">      "median[95% CI]" = meds_report,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">140</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">35</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      SIMPLIFY = FALSE</pre>
+                      <pre class="language-r">      check.names = FALSE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">141</td>
+                    <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
+                  <tr class="never">
+                    <td class="num">37</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
                   <tr class="covered">
-                    <td class="num">142</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">38</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    survminer::arrange_ggsurvplots(splots, nrow = 1 + (km_layout == "all"))</pre>
+                      <pre class="language-r">  desc_res &lt;- cbind(desc_res[c(2, 1), ], "HR[95% CI]" = c(hr_res, ""), "p-Value" = c(hr_pval, ""))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">143</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">39</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  names(desc_res)[3] &lt;- "n.events(%)" # cbind changes column name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">144</td>
+                    <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">145</td>
+                    <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # add first tag column if applicable</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">42</td>
+                    <td class="coverage">15<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  if (!is.null(tag)) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">43</td>
+                    <td class="coverage">15<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    desc_res &lt;- cbind(data.frame(Matching = rep(tag, nrow(desc_res))), desc_res)</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">44</td>
+                    <td class="coverage">15<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    desc_res$Matching[duplicated(desc_res$Matching)] &lt;- ""</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">146</td>
+                    <td class="num">45</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Basic Kaplan Meier (KM) plot function using ggplot</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">147</td>
+                    <td class="num">46</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">148</td>
+                    <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This function generates a basic KM plot using ggplot.</pre>
+                      <pre class="language-r">  # output</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">48</td>
+                    <td class="coverage">15<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  desc_res</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">149</td>
+                    <td class="num">49</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">150</td>
+                    <td class="num">50</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param kmlist a list of \code{survfit} object</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">151</td>
+                    <td class="num">51</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param kmlist_name a vector indicating the treatment names of each \code{survfit} object</pre>
+                      <pre class="language-r">#' helper function: sort out a nice report table to summarize binary analysis results</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">152</td>
+                    <td class="num">52</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param endpoint_name a string, name of time to event endpoint, to be show in the</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">153</td>
+                    <td class="num">53</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   last line of title</pre>
+                      <pre class="language-r">#' @param binobj object from glm()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">154</td>
+                    <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param show_risk_set logical, show risk set table or not, TRUE by default</pre>
+                      <pre class="language-r">#' @param weighted_result object res_AB</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">155</td>
+                    <td class="num">55</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param main_title a string, main title of the KM plot</pre>
+                      <pre class="language-r">#' @param eff_measure a string, binary effect measure, could be "OR", "RR", "RD"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">156</td>
+                    <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param break_x_by bin parameter for \code{survminer}</pre>
+                      <pre class="language-r">#' @param tag a string, by default NULL, if specified, an extra 1st column is created in the output</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">157</td>
+                    <td class="num">57</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param censor indicator to include censor information</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">158</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param xlim x limit for the x-axis of the plot</pre>
+                      <pre class="language-r">#' @return a data frame with sample size, incidence rate, estimate of binary effect measure with</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">159</td>
+                    <td class="num">59</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param use_colors a character vector of length up to 4, colors to the KM curves,</pre>
+                      <pre class="language-r">#' 95% CI and Wald test of hazard ratio</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">160</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   it will be passed to 'col' of \code{lines()}</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">161</td>
+                    <td class="num">61</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param use_line_types a numeric vector of length up to 4, line type to the KM curves,</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">162</td>
+                    <td class="num">62</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   it will be passed to \code{lty} of \code{lines()}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">163</td>
+                    <td class="num">63</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">report_table_binary &lt;- function(binobj, weighted_result = NULL, eff_measure = c("OR", "RD", "RR"), tag = NULL) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">64</td>
+                    <td class="coverage">12<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  weighted &lt;- ifelse(is.null(weighted_result), FALSE, TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">164</td>
+                    <td class="num">65</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # descriptive part</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">165</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">66</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">basic_kmplot2 &lt;- function(kmlist,</pre>
+                      <pre class="language-r">  ARM &lt;- levels(binobj$data$ARM)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">166</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">67</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          kmlist_name,</pre>
+                      <pre class="language-r">  if (!weighted) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">167</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">68</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          endpoint_name = "Time to Event Endpoint",</pre>
+                      <pre class="language-r">    N &lt;- tapply(binobj$data$USUBJID, binobj$data$ARM, length)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">168</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">69</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          show_risk_set = TRUE,</pre>
+                      <pre class="language-r">    N.EVNT &lt;- tapply(binobj$data$RESPONSE, binobj$data$ARM, sum)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">169</td>
+                    <td class="num">70</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          main_title = "Kaplan-Meier Curves",</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">170</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">71</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          break_x_by = NULL,</pre>
+                      <pre class="language-r">    N &lt;- tapply(binobj$data$weights, binobj$data$ARM, length)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">171</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">72</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          censor = TRUE,</pre>
+                      <pre class="language-r">    N.EVNT &lt;- tapply(binobj$data$weights * binobj$data$RESPONSE, binobj$data$ARM, sum)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">172</td>
+                    <td class="num">73</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          xlim = NULL,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">173</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">74</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          use_colors = NULL,</pre>
+                      <pre class="language-r">  N.EVNT.PERC &lt;- round(N.EVNT * 100 / N, 1)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">174</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">75</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          use_line_types = NULL) {</pre>
+                      <pre class="language-r">  N.EVNT &lt;- round(N.EVNT, 1)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">175</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">76</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!requireNamespace("survminer", quietly = TRUE)) stop("survminer package is required for this function")</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">176</td>
+                    <td class="num">77</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # inferential part</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">177</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">78</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(use_line_types)) {</pre>
+                      <pre class="language-r">  if (!weighted) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">178</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">79</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_line_types &lt;- c(1, 1, 2, 2)</pre>
+                      <pre class="language-r">    bin_res_est &lt;- coef(binobj)[2]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">179</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">80</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    bin_res_ci &lt;- confint(binobj, parm = 2, test = "LRT", trace = FALSE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">180</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">81</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    bin_res &lt;- c(bin_res_est, bin_res_ci)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">181</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">82</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(use_colors)) {</pre>
+                      <pre class="language-r">    if (eff_measure != "RD") bin_res &lt;- exp(bin_res)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">182</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">83</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    use_colors &lt;- c("#5450E4", "#00857C", "#6ECEB2", "#7B68EE")</pre>
+                      <pre class="language-r">    bin_res &lt;- round(bin_res, 2) |&gt; format(nsmall = 2)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">183</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">84</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    bin_res &lt;- paste0(bin_res[1], "[", bin_res[2], ";", bin_res[3], "]")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">184</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">85</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    bin_pval &lt;- round(summary(binobj)$coefficients[2, 4], 3) |&gt; format(nsmall = 3)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">185</td>
+                    <td class="num">86</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # Produce the Kaplan-Meier plot</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">186</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">87</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  survminer_plot &lt;- survminer::ggsurvplot(kmlist,</pre>
+                      <pre class="language-r">    bin_res &lt;- round(unlist(weighted_result[c("est", "ci_l", "ci_u")]), 2) |&gt; format(nsmall = 2)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">187</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">88</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    linetype = use_line_types,</pre>
+                      <pre class="language-r">    bin_res &lt;- paste0(bin_res[1], "[", bin_res[2], ";", bin_res[3], "]")</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">188</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">89</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    palette = use_colors,</pre>
+                      <pre class="language-r">    bin_pval &lt;- round(weighted_result$pval, 3) |&gt; format(nsmall = 3)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">189</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">90</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    size = 0.2,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">190</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">91</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    combine = TRUE,</pre>
+                      <pre class="language-r">  if (bin_pval == "0.000") bin_pval &lt;- "&lt;0.001"</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">191</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">92</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    risk.table = show_risk_set,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">192</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">93</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    risk.table.y.text.col = TRUE,</pre>
+                      <pre class="language-r">  # assemble the table</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">193</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">94</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    risk.table.y.text = FALSE,</pre>
+                      <pre class="language-r">  desc_res &lt;- data.frame(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">194</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">95</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    break.x.by = break_x_by,</pre>
+                      <pre class="language-r">    "treatment" = ARM,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">195</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">96</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    censor = censor,</pre>
+                      <pre class="language-r">    "N" = N,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">196</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">97</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    censor.size = 2,</pre>
+                      <pre class="language-r">    "n.events(%)" = paste0(N.EVNT, "(", format(N.EVNT.PERC, nsmall = 1), ")")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">197</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">98</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    xlab = "Time",</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">198</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">99</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ylab = endpoint_name,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">199</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">100</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    legend.title = "Treatment",</pre>
+                      <pre class="language-r">  desc_res &lt;- cbind(desc_res[c(2, 1), ], "xx[95% CI]" = c(bin_res, ""), "p-Value" = c(bin_pval, ""))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">200</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">101</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    legend = c(0.85, 0.82),</pre>
+                      <pre class="language-r">  names(desc_res)[ncol(desc_res) - 1] &lt;- paste0(eff_measure, "[95% CI]")</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">201</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">102</td>
+                    <td class="coverage">12<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  names(desc_res)[3] &lt;- "n.events(%)" # cbind changes column name</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">103</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    title = paste0(main_title, "\nEndpoint: ", endpoint_name),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">202</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">104</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    legend.labs = kmlist_name,</pre>
+                      <pre class="language-r">  # add first tag column if applicable</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">203</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">105</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    tables.theme = survminer::theme_cleantable(),</pre>
+                      <pre class="language-r">  if (!is.null(tag)) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">204</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">106</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ggtheme = ggplot2::theme_classic(base_size = 10),</pre>
+                      <pre class="language-r">    desc_res &lt;- cbind(data.frame(Matching = rep(tag, nrow(desc_res))), desc_res)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">205</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">107</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    fontsize = 3,</pre>
+                      <pre class="language-r">    desc_res$Matching[duplicated(desc_res$Matching)] &lt;- ""</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">206</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">108</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    conf.int = FALSE,</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">207</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">109</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    xlim = xlim</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">208</td>
+                    <td class="num">110</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">  # output</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">209</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">111</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  survminer_plot</pre>
+                      <pre class="language-r">  desc_res</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">210</td>
+                    <td class="num">112</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
@@ -21604,14 +23697,14 @@ <h2>maicplus coverage - 54.75%</h2>
                 </tbody>
               </table>
             </div>
-            <div id="R/data_generation.R" class="hidden">
+            <div id="R/bootstrap.R" class="hidden">
               <table class="table-condensed">
                 <tbody>
                   <tr class="never">
                     <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Generate time-to-event data</pre>
+                      <pre class="language-r">#' Bootstrapping weighted hazard ratios to obtain confidence interval</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -21625,175 +23718,175 @@ <h2>maicplus coverage - 54.75%</h2>
                     <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Function generates time-to-event data. We follow the data-generating mechanism from</pre>
+                      <pre class="language-r">#' This function uses \code{\link{boot}} to resample internal IPD data</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Bender et al. and Remiro-Azocar et al. 2021 to simulate Weibull-distributed survival times</pre>
+                      <pre class="language-r">#' to obtain bootstrapped hazard ratio values which is used to form confidence</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' under a proportional hazards parameterization. As per Remiro-Azocar et al, we set the</pre>
+                      <pre class="language-r">#' interval. Note that due to lack of full IPD of covariates in the</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' default scale parameter (lambda) to 8.5 and shape parameter (nu) to 1.3 to reflect frequently</pre>
+                      <pre class="language-r">#' aggregate data, pseudo IPD will not be bootstrapped.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' observed mortality trends in metastatic cancer patients. Censoring times are generated from</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' exponential distribution where the rate parameter is 0.96 is selected to achieve a censoring rate</pre>
+                      <pre class="language-r">#' @param ipd_centered A data frame containing individual patient data</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' of 35% under the active treatment at baseline (with the values of the covariates set to zero).</pre>
+                      <pre class="language-r">#'   from the internal IPD study. This data frame should have already been</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   centered using [center_ipd] function</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param N sample size</pre>
+                      <pre class="language-r">#' @param i Index used to select a sample within \code{\link{boot}}.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ncov number of covariates to generate</pre>
+                      <pre class="language-r">#' @param centered_colnames A character vector giving the names of the covariates to use in matching.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param lambda scale parameter in baseline hazard function</pre>
+                      <pre class="language-r">#'  These names must match the column names in internal dataset.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param nu shape parameter in baseline hazard function</pre>
+                      <pre class="language-r">#' @param pseudo_ipd A data frame containing pseudo individual patient data</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param censor_rate rate parameter of the exponential distribution of censoring times</pre>
+                      <pre class="language-r">#'   from the comparator study needed to derive the relative treatment effect.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param cor correlation between covariates</pre>
+                      <pre class="language-r">#'   Pseudo IPD is only used for unanchored case. pseudo_ipd should have time, event,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param marginal_mean marginal mean of covariates</pre>
+                      <pre class="language-r">#'   and ARM variable with a same name and order as that of ipd_centered</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param marginal_sd marginal standard deviation of covariates</pre>
+                      <pre class="language-r">#' @param model Survival model to run to calculate HR with correct time, event, and #'   ARM names</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param beta vector of coefficients for prognostic factors. Defaults is `-log(0.67)` for all covariates.</pre>
+                      <pre class="language-r">#' @param ref_treat Reference treatment for the survival model</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param gamma vector of coefficients for effect modifiers. Default is `0` for half of the covariates and</pre>
+                      <pre class="language-r">#' @param min_weight A numeric value that defines the minimum weight allowed.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'  `-log(0.67)` for the others.</pre>
+                      <pre class="language-r">#'   This value (default 0.0001) will replace weights estimated at 0 in a sample.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param d0 coefficient for the treatment effect for patients with `treat = 0`</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param seed seed used for simulation reproducibility</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' # Unanchored example</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return data.frame with survival time, censor (event) status, treatment indicator, and covariates</pre>
+                      <pre class="language-r">#' load(system.file("extdata", "ipd.rda", package = "maicplus", mustWork = TRUE))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' load(system.file("extdata", "agd.rda", package = "maicplus", mustWork = TRUE))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @references Remiro-Azocar et al. 2021</pre>
+                      <pre class="language-r">#' ipd_centered &lt;- center_ipd(ipd = ipd, agd = agd)</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -21807,737 +23900,604 @@ <h2>maicplus coverage - 54.75%</h2>
                     <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' pseudo_ipd &lt;- read.csv(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   system.file("extdata", "psuedo_IPD.csv", package = "maicplus", mustWork = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">generate_survival_data &lt;- function(N = 150, ncov = 4, lambda = 8.5, nu = 1.3, censor_rate = 0.96,</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                   cor = 0.35, marginal_mean = 0.6, marginal_sd = 0.2,</pre>
+                      <pre class="language-r">#' pseudo_ipd$ARM &lt;- "B" # Need to specify ARM for pseudo ipd</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                   beta = rep(-log(0.67), ncov),</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">34</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">                                   gamma = sort(rep(c(0, -log(0.67)), length = ncov)),</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">35</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">                                   d0 = log(0.25), seed = 1) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">36</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  set.seed(seed)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">37</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">38</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  # if beta and gamma is not specified, give it default values</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">39</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(beta)) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">40</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    beta &lt;- rep(-log(0.67), ncov)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">41</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">42</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">43</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (is.null(gamma)) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">44</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    gamma &lt;- rep(-log(0.67), ncov)</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">45</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    gamma[1:round(ncov / 2)] &lt;- 0</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">46</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">47</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">48</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  # generate ncov covariates (X) using a multivariate normal</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">49</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  sigma &lt;- matrix(cor, nrow = ncov, ncol = ncov)</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">50</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  diag(sigma) &lt;- 1</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">51</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  sigma &lt;- sigma * marginal_sd^2</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">52</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">53</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">34</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  covariates &lt;- MASS::mvrnorm(N, mu = rep(marginal_mean, ncov), Sigma = sigma)</pre>
+                      <pre class="language-r">#' # Need to ensure pseudo_ipd and ipd_matched have same names</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">54</td>
+                    <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' colnames(pseudo_ipd) &lt;- c("TIME", "EVENT", "ARM")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">55</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">36</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  treat &lt;- sample(x = c(0, 1), size = N, replace = TRUE, prob = c(0.5, 0.5))</pre>
+                      <pre class="language-r">#' \dontrun{</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">56</td>
+                    <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' HR_bootstraps &lt;- boot(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">57</td>
+                    <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # linear predictor</pre>
+                      <pre class="language-r">#'   data = ipd_centered,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">58</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">39</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  lp &lt;- covariates %*% beta + covariates %*% gamma * treat + d0 * treat</pre>
+                      <pre class="language-r">#'   statistic = bootstrap_HR,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">59</td>
+                    <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   centered_colnames = centered_colnames,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">60</td>
+                    <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # Weibull latent event times</pre>
+                      <pre class="language-r">#'   pseudo_ipd = pseudo_ipd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">61</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">42</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  u &lt;- runif(n = N)</pre>
+                      <pre class="language-r">#'   model = Surv(TIME, EVENT == 1) ~ ARM,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">62</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">43</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  latent_time &lt;- (-log(u) / (lambda * exp(lp)))^(1 / nu)</pre>
+                      <pre class="language-r">#'   ref_treat = "B",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">63</td>
+                    <td class="num">44</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   R = 1000</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">64</td>
+                    <td class="num">45</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # exponential censoring times</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">65</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">46</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  censor_time &lt;- rexp(n = N, rate = censor_rate)</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">66</td>
+                    <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @return The HR bootstraps</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">67</td>
+                    <td class="num">48</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # follow-up times and event indicators</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">68</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">49</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  time &lt;- pmin(latent_time, censor_time)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">69</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">50</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  event &lt;- as.numeric(latent_time &lt;= censor_time)</pre>
+                      <pre class="language-r">bootstrap_HR &lt;- function(ipd_centered, i, centered_colnames,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">70</td>
+                    <td class="num">51</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                         pseudo_ipd = NULL, model,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">71</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">52</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  colnames(covariates) &lt;- paste0("x", seq_len(ncov))</pre>
+                      <pre class="language-r">                         min_weight = 0.0001, ref_treat = NULL) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">72</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">53</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  survival_data &lt;- data.frame(USUBJID = seq_len(N), time = time, event = event, treat = treat, x = covariates)</pre>
+                      <pre class="language-r">  # Resamples the centered internal IPD data</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">73</td>
+                    <td class="num">54</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  return(survival_data)</pre>
+                      <pre class="language-r">  bootstrap_data &lt;- ipd_centered[i, ]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">74</td>
+                    <td class="num">55</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/zzz.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">.onLoad &lt;- function(libname, pkgname) {</pre>
+                      <pre class="language-r">  # Estimates weights</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">2</td>
+                    <td class="num">57</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  set_time_conversion()</pre>
+                      <pre class="language-r">  weighted_data &lt;- estimate_weights(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">3</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">58</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">    data = bootstrap_data,</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/time-helper.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
-                  <tr class="never">
-                    <td class="num">1</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">59</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># Create an environment for settings</pre>
+                      <pre class="language-r">    centered_colnames = centered_colnames</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">2</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">settings_env &lt;- new.env()</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">61</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">4</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">62</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Get and Set Time Conversion Factors</pre>
+                      <pre class="language-r">  ipd_matched &lt;- weighted_data$data</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">5</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">63</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  if (length(unique(ipd_matched$ARM)) == 2) { # this is the anchored case</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">6</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">64</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param days Factor to divide data time units to get time in days</pre>
+                      <pre class="language-r">    combined_data &lt;- ipd_matched</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">65</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param weeks Factor to divide data time units to get time in weeks</pre>
+                      <pre class="language-r">  } else if (length(unique(ipd_matched$ARM)) == 1) { # this is the unanchored case</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">8</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">66</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param months Factor to divide data time units to get time in months</pre>
+                      <pre class="language-r">    if (is.null(pseudo_ipd)) stop("For unanchored case pseudo_ipd needs to be specified")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">9</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">67</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param years Factor to divide data time units to get time in years</pre>
+                      <pre class="language-r">    if (is.null(pseudo_ipd$ARM)) stop("external data should have an ARM column")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">10</td>
+                    <td class="num">68</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">11</td>
+                    <td class="num">69</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return No value returned. Conversion factors are stored internally and used within functions.</pre>
+                      <pre class="language-r">    # Assign weight of 1 for pseudo_ipd if it not defined already</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">70</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">    pseudo_ipd$weights &lt;- 1</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">13</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">71</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @rdname time_conversion</pre>
+                      <pre class="language-r">    combined_data &lt;- rbind(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">14</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">72</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      ipd_matched[, colnames(pseudo_ipd)],</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">15</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">73</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">      pseudo_ipd</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">16</td>
+                    <td class="num">74</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Native time format is years</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">17</td>
+                    <td class="num">75</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' set_time_conversion(days = 1 / 365.25, weeks = 1 / 52.17857, months = 1 / 12, years = 1)</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">18</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">76</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    stop("ipd_matched ARM should have 1 or 2 treatments")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">19</td>
+                    <td class="num">77</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Native time format is days</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">20</td>
+                    <td class="num">78</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' set_time_conversion(days = 1, weeks = 7, months = 365.25 / 12, years = 365.25)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">21</td>
+                    <td class="num">79</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">set_time_conversion &lt;- function(days = 1, weeks = 7, months = 365.25 / 12, years = 365.25) {</pre>
+                      <pre class="language-r">  # set the base treatment</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">22</td>
+                    <td class="num">80</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  settings_env$time_conversion &lt;- c(days = days, weeks = weeks, months = months, years = years)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">23</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  if (is.null(ref_treat)) stop("Need to specify a value for ref_treat")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">24</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">81</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  combined_data$ARM &lt;- stats::relevel(as.factor(combined_data$ARM), ref = ref_treat)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">25</td>
+                    <td class="num">82</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">83</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param factor Time factor to get.</pre>
+                      <pre class="language-r">  # set weights that are below min_weight to min_weight to avoid issues with 0 values</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">27</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">84</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @rdname time_conversion</pre>
+                      <pre class="language-r">  combined_data$weights &lt;- ifelse(combined_data$weights &lt; min_weight, min_weight, combined_data$weights)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">28</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">85</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">  cox_model &lt;- survival::coxph(model, data = combined_data, weights = weights, robust = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">29</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">86</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  HR &lt;- exp(cox_model$coefficients)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">30</td>
+                    <td class="num">87</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">31</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">88</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Get time scale factors:</pre>
+                      <pre class="language-r">  return(HR)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">89</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' get_time_conversion("years")</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/utils.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
                   <tr class="never">
-                    <td class="num">33</td>
+                    <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' get_time_conversion("weeks")</pre>
+                      <pre class="language-r"># Restore the RNG back to a previous state using the global .Random.seed</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">34</td>
+                    <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">get_time_conversion &lt;- function(factor = c("days", "weeks", "months", "years")) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">35</td>
-                    <td class="coverage">20<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  factor &lt;- match.arg(factor, several.ok = TRUE)</pre>
+                      <pre class="language-r">set_random_seed &lt;- function(old_seed) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">36</td>
-                    <td class="coverage">20<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  if (!exists("time_conversion", settings_env)) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">37</td>
-                    <td class="coverage">!</td>
+                    <td class="num">3</td>
+                    <td class="coverage">14<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    warning("No time conversion factors previously set. Setting defaults.")</pre>
+                      <pre class="language-r">  if (is.null(old_seed)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">38</td>
+                    <td class="num">4</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    set_time_conversion()</pre>
+                      <pre class="language-r">    rm(".Random.seed", envir = globalenv(), inherits = FALSE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">39</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">40</td>
-                    <td class="coverage">20<em>x</em></td>
+                    <td class="num">6</td>
+                    <td class="coverage">14<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  settings_env$time_conversion[factor]</pre>
+                      <pre class="language-r">    assign(".Random.seed", value = old_seed, envir = globalenv(), inherits = FALSE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">41</td>
+                    <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">42</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">43</td>
+                    <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">44</td>
+                    <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Convert Time Values Using Scaling Factors</pre>
+                      <pre class="language-r">construct_boot_data &lt;- function(weighted_data, i = 1) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">45</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">11</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  if (is.null(weighted_data$boot)) stop("Must contain bootstrap results from estimate_weights()")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">46</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">12</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param times Numeric time values</pre>
+                      <pre class="language-r">  i &lt;- as.integer(i)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">47</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">13</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param as A time scale to convert to</pre>
+                      <pre class="language-r">  R &lt;- dim(weighted_data$boot)[3]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">48</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">14</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  if (i &lt; 1 || i &gt; R) stop("i must be integer between 1 and ", R)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">49</td>
+                    <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Returns a numeric vector calculated from `times / get_time_conversion(factor = as)`</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">50</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">16</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  boot_data &lt;- weighted_data$boot[, , i]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">51</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">17</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">get_time_as &lt;- function(times, as = c("days", "weeks", "months", "years")) {</pre>
+                      <pre class="language-r">  weighted_data$data &lt;- weighted_data$data[boot_data[, 1], ]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">52</td>
+                    <td class="num">18</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!is.numeric(times)) stop("times arguments must be numeric")</pre>
+                      <pre class="language-r">  weighted_data$data$weights &lt;- boot_data[, 2]</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">53</td>
-                    <td class="coverage">20<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">19</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  as &lt;- match.arg(as)</pre>
+                      <pre class="language-r">  weighted_data$data$scaled_weights &lt;- boot_data[, 2] / sum(boot_data[, 2])</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">54</td>
-                    <td class="coverage">20<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">20</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  times / get_time_conversion(as)</pre>
+                      <pre class="language-r">  weighted_data</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">55</td>
+                    <td class="num">21</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">}</pre>
+                    </td>
+                  </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/zzz.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
+                  <tr class="never">
+                    <td class="num">1</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">.onLoad &lt;- function(libname, pkgname) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">2</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  set_time_conversion()</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>