From 125c86621290426c17b990d912e509af2c6d039d Mon Sep 17 00:00:00 2001
From: gravesti <gravesti@users.noreply.github.com>
Date: Thu, 18 Jul 2024 10:19:32 +0000
Subject: [PATCH] deploy: 862208ea3a8c3c931f2a12661fab2d05222471e7

---
 main/coverage-report/index.html | 320 ++++++++++++++++----------------
 1 file changed, 160 insertions(+), 160 deletions(-)

diff --git a/main/coverage-report/index.html b/main/coverage-report/index.html
index bdadcc44..b1403180 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 - 49.44%</h2>
+    <h2>maicplus coverage - 54.75%</h2>
     <div class="tabbable">
       <ul class="nav nav-tabs" data-tabsetid="covr">
         <li class="active">
@@ -107,8 +107,8 @@ <h2>maicplus coverage - 49.44%</h2>
       </ul>
       <div class="tab-content" data-tabsetid="covr">
         <div class="tab-pane active" title="Files" data-value="Files" id="tab-covr-1">
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+          <div class="datatables html-widget html-fill-item" id="htmlwidget-434add24dfcec78306c2" style="width:100%;height:500px;"></div>
+          <script type="application/json" data-for="htmlwidget-434add24dfcec78306c2">{"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/maic_anchored.R<\/a>","<a href=\"#\">R/binary-helper.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>"],[89,74,3,21,749,532,55,281,210,305,86,430,83,162,112],[21,20,1,12,387,224,9,97,95,161,50,224,28,48,56],[0,0,0,2,67,91,5,55,76,130,43,195,25,45,55],[21,20,1,10,320,133,4,42,19,31,7,29,3,3,1],["0","0","0","2","0","34","9","5","1","2","2","20","10","5","9"],["0.00%","0.00%","0.00%","16.67%","17.31%","40.62%","55.56%","56.70%","80.00%","80.75%","86.00%","87.05%","89.29%","93.75%","98.21%"]],"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>
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         <div class="tab-pane" title="Source" data-value="Source" id="tab-covr-2">
           <div id="files">
@@ -20488,30 +20488,30 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">52</td>
-                    <td class="coverage">!</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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">53</td>
-                    <td class="coverage">!</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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">54</td>
-                    <td class="coverage">!</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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">55</td>
-                    <td class="coverage">!</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>
                     </td>
@@ -20530,9 +20530,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">  # pre check</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">58</td>
-                    <td class="coverage">!</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>
                     </td>
@@ -20551,9 +20551,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">61</td>
-                    <td class="coverage">!</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>
                     </td>
@@ -20572,9 +20572,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">64</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<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>
                     </td>
@@ -20593,9 +20593,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">67</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<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>
                     </td>
@@ -20614,37 +20614,37 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">  # preparing data</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">70</td>
-                    <td class="coverage">!</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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">71</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">72</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">73</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<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$USUBJID)]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">74</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  tte_pseudo_ipd$weights &lt;- 1</pre>
                     </td>
@@ -20656,37 +20656,37 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">76</td>
-                    <td class="coverage">!</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="missed">
+                  <tr class="covered">
                     <td class="num">77</td>
-                    <td class="coverage">!</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="missed">
+                  <tr class="covered">
                     <td class="num">78</td>
-                    <td class="coverage">!</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="missed">
+                  <tr class="covered">
                     <td class="num">79</td>
-                    <td class="coverage">!</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="missed">
+                  <tr class="covered">
                     <td class="num">80</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></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>
                     </td>
@@ -20698,9 +20698,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">    } else {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">82</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      survfit(Surv(TIME, EVENT) ~ 1, data = data, conf.type = km_conf_type)</pre>
                     </td>
@@ -20726,9 +20726,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">86</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!is_anchored) {</pre>
                     </td>
@@ -20782,58 +20782,58 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">    basic_kmplot2(kmlist, kmlist_name, ...)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">94</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  } else if (is_anchored) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">95</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    all_km &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">96</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">97</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">98</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">99</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">100</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></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>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">101</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></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>
                     </td>
@@ -20852,44 +20852,44 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">104</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    kmlist_combined &lt;- list()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">105</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    if (km_layout %in% c("by_trial", "all")) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">106</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      kmlist_1_2 &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">107</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        setNames(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">108</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">          all_km[c(4, 1, 3, 5)],</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">109</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">          c(trt_ipd, trt_common, paste0(trt_ipd, " (weighted)"), paste0(trt_common, " (weighted)"))</pre>
                     </td>
@@ -20901,9 +20901,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">        ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">111</td>
-                    <td class="coverage">!</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>
@@ -20915,23 +20915,23 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">113</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      names(kmlist_1_2) &lt;- c(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">114</td>
-                    <td class="coverage">!</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="missed">
+                  <tr class="covered">
                     <td class="num">115</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></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>
                     </td>
@@ -20943,9 +20943,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">117</td>
-                    <td class="coverage">!</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>
@@ -20957,9 +20957,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">119</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    if (km_layout %in% c("by_arm", "all")) {</pre>
                     </td>
@@ -21034,9 +21034,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">130</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    if (km_layout == "all") {</pre>
                     </td>
@@ -21062,51 +21062,51 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">134</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    splots &lt;- mapply(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">135</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      FUN = basic_kmplot2,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">136</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      kmlist = kmlist_combined,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">137</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      kmlist_name = lapply(kmlist_combined, names),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">138</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      main_title = names(kmlist_combined),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">139</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      MoreArgs = list(...),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">140</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      SIMPLIFY = FALSE</pre>
                     </td>
@@ -21118,9 +21118,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">142</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    survminer::arrange_ggsurvplots(splots, nrow = 1 + (km_layout == "all"))</pre>
                     </td>
@@ -21363,16 +21363,16 @@ <h2>maicplus coverage - 49.44%</h2>
                       <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">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (is.null(use_line_types)) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">178</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    use_line_types &lt;- c(1, 1, 2, 2)</pre>
                     </td>
@@ -21391,16 +21391,16 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">181</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (is.null(use_colors)) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">182</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    use_colors &lt;- c("#5450E4", "#00857C", "#6ECEB2", "#7B68EE")</pre>
                     </td>
@@ -21426,156 +21426,156 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">  # Produce the Kaplan-Meier plot</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">186</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  survminer_plot &lt;- survminer::ggsurvplot(kmlist,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">187</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    linetype = use_line_types,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">188</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    palette = use_colors,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">189</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    size = 0.2,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">190</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    combine = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">191</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    risk.table = show_risk_set,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">192</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    risk.table.y.text.col = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">193</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    risk.table.y.text = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">194</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    break.x.by = break_x_by,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">195</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    censor = censor,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">196</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    censor.size = 2,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">197</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    xlab = "Time",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">198</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    ylab = endpoint_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">199</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    legend.title = "Treatment",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">200</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    legend = c(0.85, 0.82),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">201</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    title = paste0(main_title, "\nEndpoint: ", endpoint_name),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">202</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    legend.labs = kmlist_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">203</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    tables.theme = survminer::theme_cleantable(),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">204</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    ggtheme = ggplot2::theme_classic(base_size = 10),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">205</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    fontsize = 3,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">206</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    conf.int = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">207</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    xlim = xlim</pre>
                     </td>
@@ -21587,9 +21587,9 @@ <h2>maicplus coverage - 49.44%</h2>
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">209</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  survminer_plot</pre>
                     </td>
@@ -22398,14 +22398,14 @@ <h2>maicplus coverage - 49.44%</h2>
                   </tr>
                   <tr class="covered">
                     <td class="num">35</td>
-                    <td class="coverage">14<em>x</em></td>
+                    <td class="coverage">16<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  factor &lt;- match.arg(factor, several.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">36</td>
-                    <td class="coverage">14<em>x</em></td>
+                    <td class="coverage">16<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  if (!exists("time_conversion", settings_env)) {</pre>
                     </td>
@@ -22433,7 +22433,7 @@ <h2>maicplus coverage - 49.44%</h2>
                   </tr>
                   <tr class="covered">
                     <td class="num">40</td>
-                    <td class="coverage">14<em>x</em></td>
+                    <td class="coverage">16<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  settings_env$time_conversion[factor]</pre>
                     </td>
@@ -22524,14 +22524,14 @@ <h2>maicplus coverage - 49.44%</h2>
                   </tr>
                   <tr class="covered">
                     <td class="num">53</td>
-                    <td class="coverage">14<em>x</em></td>
+                    <td class="coverage">16<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  as &lt;- match.arg(as)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">54</td>
-                    <td class="coverage">14<em>x</em></td>
+                    <td class="coverage">16<em>x</em></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  times / get_time_conversion(as)</pre>
                     </td>