preparation for version 0.9.5 cran submission

billdenney · Oct 29, 2021 · d5eabf4 · d5eabf4
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diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,5 @@
 doc
 Meta
 docs
+/doc/
+/Meta/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PKNCA
 Type: Package
 Title: Perform Pharmacokinetic Non-Compartmental Analysis
-Version: 0.9.4.9001
+Version: 0.9.5
 Authors@R: c(
     person("Bill", "Denney", email="wdenney@humanpredictions.com", role=c("aut", "cre"), comment=c(ORCID="0000-0002-5759-428X")),
     person("Clare", "Buckeridge", email="clare.buckeridge@pfizer.com", role="aut"),
@@ -27,9 +27,10 @@ Suggests:
 Description: Compute standard Non-Compartmental Analysis (NCA) parameters for
     typical pharmacokinetic analyses and summarize them.
 License: AGPL-3
-URL: http://billdenney.github.io/pknca, https://github.com/billdenney/pknca
+URL: https://billdenney.github.io/pknca/, https://github.com/billdenney/pknca
 BugReports: https://github.com/billdenney/pknca/issues
 NeedsCompilation: no
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Encoding: UTF-8
+Language: en-US
diff --git a/NAMESPACE b/NAMESPACE
@@ -11,8 +11,6 @@ S3method(PKNCAdose,data.frame)
 S3method(PKNCAdose,default)
 S3method(PKNCAdose,tbl_df)
 S3method(as.data.frame,PKNCAresults)
-S3method(dplyr::group_vars,PKNCAconc)
-S3method(dplyr::group_vars,PKNCAdose)
 S3method(exclude,default)
 S3method(formula,PKNCAconc)
 S3method(formula,PKNCAdose)

diff --git a/NEWS.md b/NEWS.md
@@ -14,7 +14,7 @@ the dosing including dose amount and route.
     and PKNCAdose objects were removed along with the merge.splitList function.
 * Single-subject (ungrouped) analysis works without creating a dummy group (#74)
 * PKNCAconc objects are checked earlier for valid data (#154)
-* Add time_above parameter to calcualte time above a given concentration.
+* Add time_above parameter to calculate time above a given concentration.
 * Fix numeric BLQ replacement when the value is a number and different values
   are given for first, middle, and last (related to #145).  This only affects
   datasets where BLQ is being replaced with a nonzero value (not a common

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 <!-- badges: start -->
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/PKNCA)](https://cran.r-project.org/package=PKNCA)
 [![R build status](https://github.com/billdenney/pknca/workflows/R-CMD-check/badge.svg)](https://github.com/billdenney/pknca/actions)
-[![Code_Coverage_Badge](http://codecov.io/github/billdenney/pknca/coverage.svg?branch=master)](http://codecov.io/github/billdenney/pknca?branch=master)
+[![Code_Coverage_Badge](https://codecov.io/github/billdenney/pknca/coverage.svg?branch=master)](https://codecov.io/github/billdenney/pknca?branch=master)
 [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/2054/badge)](https://bestpractices.coreinfrastructure.org/projects/2054)
 <!-- badges: end -->
 

diff --git a/doc/AUC-Calculation-with-PKNCA.html b/doc/AUC-Calculation-with-PKNCA.html
diff --git a/doc/Example-theophylline.html b/doc/Example-theophylline.html
diff --git a/doc/Half-Life-Calculation.html b/doc/Half-Life-Calculation.html
diff --git a/doc/Introduction-and-Usage.html b/doc/Introduction-and-Usage.html
diff --git a/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.html b/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.html
@@ -1,209 +1,37 @@
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+<meta name="viewport" content="width=device-width, initial-scale=1" />
 
 <meta name="author" content="Bill Denney" />
 
 
 <title>Methods Used for Dose-Aware Concentration Interpolation/Extrapolation</title>
 
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@@ -222,7 +50,8 @@ <h4 class="author">Bill Denney</h4>
 <div id="TOC">
 <ul>
 <li><a href="#introduction">Introduction</a></li>
-<li><a href="#methods">Methods</a><ul>
+<li><a href="#methods">Methods</a>
+<ul>
 <li><a href="#observed-concentration">Observed concentration</a></li>
 <li><a href="#impossible-combinations">Impossible combinations</a></li>
 <li><a href="#doses-with-no-concentrations-between">Doses with no concentrations between</a></li>
@@ -1517,6 +1346,12 @@ <h2>Dose before, concentration after without a dose</h2>
 <div id="appendix-complete-methods-table" class="section level1">
 <h1>Appendix: Complete Methods Table</h1>
 <table>
+<colgroup>
+<col width="16%" />
+<col width="16%" />
+<col width="16%" />
+<col width="50%" />
+</colgroup>
 <thead>
 <tr class="header">
 <th align="left">Event Before</th>
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,3 +5,5 @@ @@
     doc
     Meta
     docs
+    /doc/
+    /Meta/