include covr in build

.Rbuildignore

@@ -15,3 +15,4 @@
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
 ^drafts$
+^codecov\.yml$

DESCRIPTION

@@ -20,6 +20,7 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 LazyData: true
 Suggests:
+    covr,
     knitr,
     rmarkdown,
     spelling,

README.md

@@ -4,7 +4,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7572023.svg)](https://doi.org/10.5281/zenodo.7572023)
 [![Github Actions](https://github.com/agdamsbo/stRoke/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/agdamsbo/stRoke/actions/workflows/R-CMD-check.yaml)
 [![Page deployed](https://github.com/agdamsbo/stRoke/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/agdamsbo/stRoke/actions/workflows/pages/pages-build-deployment)
-[![codecov](https://codecov.io/github/agdamsbo/stRoke/branch/main/graph/badge.svg?token=U0RBZYSKG5)](https://codecov.io/github/agdamsbo/stRoke)
+[![Codecov test coverage](https://codecov.io/gh/agdamsbo/stRoke/branch/main/graph/badge.svg)](https://app.codecov.io/gh/agdamsbo/stRoke?branch=main)
 [![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/stRoke)](https://cran.r-project.org/package=stRoke)
 <!-- badges: end -->
 

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

cran-comments.md

@@ -1,17 +1,15 @@
-For a CRAN submission we recommend that you fix all NOTEs, WARNINGs and ERRORs.
+####
+This is a new package version
+
 ## Test environments
 - R-hub windows-x86_64-devel (r-devel)
 - R-hub ubuntu-gcc-release (r-release)
 - R-hub fedora-clang-devel (r-devel)
 
 ## R CMD check results
-❯ On windows-x86_64-devel (r-devel)
-  checking CRAN incoming feasibility ... [22s] NOTE
-
 ❯ On windows-x86_64-devel (r-devel)
   checking for detritus in the temp directory ... NOTE
   Found the following files/directories:
-  
     'lastMiKTeXException'
 
 ❯ On ubuntu-gcc-release (r-release)
@@ -19,10 +17,6 @@ For a CRAN submission we recommend that you fix all NOTEs, WARNINGs and ERRORs.
   Maintainer: ‘Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>’
   
   Found the following (possibly) invalid URLs:
-    URL: https://beta.openai.com/overview (moved to https://platform.openai.com/overview)
-      From: inst/doc/toolbox.html
-      Status: 200
-      Message: OK
     URL: https://doi.org/10.1161/STROKEAHA.117.020067
       From: inst/doc/toolbox.html
       Status: 403
@@ -43,34 +37,9 @@ For a CRAN submission we recommend that you fix all NOTEs, WARNINGs and ERRORs.
       Status: Forbidden
       Message: 403
 
-❯ On ubuntu-gcc-release (r-release)
-  checking examples ... [13s/58s] NOTE
-  Examples with CPU (user + system) or elapsed time > 5s
-                  user system elapsed
-  generic_stroke 4.556  0.082  22.210
-  label_select   1.648  0.008   7.649
-  ci_plot        1.441  0.028   6.253
-
-❯ On fedora-clang-devel (r-devel)
-  checking CRAN incoming feasibility ... [10s/73s] NOTE
-  Maintainer: ‘Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>’
-  
-  Found the following (possibly) invalid URLs:
-    URL: https://beta.openai.com/overview (moved to https://platform.openai.com/overview)
-      From: inst/doc/toolbox.html
-      Status: 200
-      Message: OK
-
-❯ On fedora-clang-devel (r-devel)
-  checking examples ... [13s/56s] NOTE
-  Examples with CPU (user + system) or elapsed time > 5s
-                  user system elapsed
-  generic_stroke 4.819  0.063  21.203
-  label_select   1.557  0.007   6.411
-  ci_plot        1.494  0.009   6.765
-
 ❯ On fedora-clang-devel (r-devel)
   checking HTML version of manual ... NOTE
   Skipping checking HTML validation: no command 'tidy' found
 
-0 errors ✔ | 0 warnings ✔ | 7 notes ✖
+0 errors ✔ | 0 warnings ✔ | 3 notes ✖
+

docs/articles/Toolbox.html

@@ -216,12 +216,12 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span>               variables <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"hypertension"</span>, <span class="st">"diabetes"</span>, <span class="st">"civil"</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; Waiting for profiling to be done...</span></span>
 <span><span class="co">#&gt; $`Table 1`</span></span>
-<span><span class="co">#&gt; &lt;div id="zlonxkjxpy" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"&gt;</span></span>
+<span><span class="co">#&gt; &lt;div id="fzlccdqrrt" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"&gt;</span></span>
 <span><span class="co">#&gt;   &lt;style&gt;html {</span></span>
 <span><span class="co">#&gt;   font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Helvetica Neue', 'Fira Sans', 'Droid Sans', Arial, sans-serif;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_table {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_table {</span></span>
 <span><span class="co">#&gt;   display: table;</span></span>
 <span><span class="co">#&gt;   border-collapse: collapse;</span></span>
 <span><span class="co">#&gt;   margin-left: auto;</span></span>
@@ -246,7 +246,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   border-left-color: #D3D3D3;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_heading {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_heading {</span></span>
 <span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
 <span><span class="co">#&gt;   text-align: center;</span></span>
 <span><span class="co">#&gt;   border-bottom-color: #FFFFFF;</span></span>
@@ -258,12 +258,12 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   border-right-color: #D3D3D3;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_caption {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_caption {</span></span>
 <span><span class="co">#&gt;   padding-top: 4px;</span></span>
 <span><span class="co">#&gt;   padding-bottom: 4px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_title {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_title {</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   font-size: 125%;</span></span>
 <span><span class="co">#&gt;   font-weight: initial;</span></span>
@@ -275,7 +275,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   border-bottom-width: 0;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_subtitle {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_subtitle {</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   font-size: 85%;</span></span>
 <span><span class="co">#&gt;   font-weight: initial;</span></span>
@@ -287,13 +287,13 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   border-top-width: 0;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_bottom_border {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_bottom_border {</span></span>
 <span><span class="co">#&gt;   border-bottom-style: solid;</span></span>
 <span><span class="co">#&gt;   border-bottom-width: 2px;</span></span>
 <span><span class="co">#&gt;   border-bottom-color: #D3D3D3;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_col_headings {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_col_headings {</span></span>
 <span><span class="co">#&gt;   border-top-style: solid;</span></span>
 <span><span class="co">#&gt;   border-top-width: 2px;</span></span>
 <span><span class="co">#&gt;   border-top-color: #D3D3D3;</span></span>
@@ -308,7 +308,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   border-right-color: #D3D3D3;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_col_heading {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_col_heading {</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
 <span><span class="co">#&gt;   font-size: 100%;</span></span>
@@ -328,7 +328,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   overflow-x: hidden;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_column_spanner_outer {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_column_spanner_outer {</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
 <span><span class="co">#&gt;   font-size: 100%;</span></span>
@@ -340,15 +340,15 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   padding-right: 4px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_column_spanner_outer:first-child {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_column_spanner_outer:first-child {</span></span>
 <span><span class="co">#&gt;   padding-left: 0;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_column_spanner_outer:last-child {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_column_spanner_outer:last-child {</span></span>
 <span><span class="co">#&gt;   padding-right: 0;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_column_spanner {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_column_spanner {</span></span>
 <span><span class="co">#&gt;   border-bottom-style: solid;</span></span>
 <span><span class="co">#&gt;   border-bottom-width: 2px;</span></span>
 <span><span class="co">#&gt;   border-bottom-color: #D3D3D3;</span></span>
@@ -360,7 +360,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   width: 100%;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_group_heading {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_group_heading {</span></span>
 <span><span class="co">#&gt;   padding-top: 8px;</span></span>
 <span><span class="co">#&gt;   padding-bottom: 8px;</span></span>
 <span><span class="co">#&gt;   padding-left: 5px;</span></span>
@@ -386,7 +386,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   text-align: left;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_empty_group_heading {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_empty_group_heading {</span></span>
 <span><span class="co">#&gt;   padding: 0.5px;</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
@@ -401,15 +401,15 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   vertical-align: middle;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_from_md &gt; :first-child {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_from_md &gt; :first-child {</span></span>
 <span><span class="co">#&gt;   margin-top: 0;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_from_md &gt; :last-child {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_from_md &gt; :last-child {</span></span>
 <span><span class="co">#&gt;   margin-bottom: 0;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_row {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_row {</span></span>
 <span><span class="co">#&gt;   padding-top: 8px;</span></span>
 <span><span class="co">#&gt;   padding-bottom: 8px;</span></span>
 <span><span class="co">#&gt;   padding-left: 5px;</span></span>
@@ -428,7 +428,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   overflow-x: hidden;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_stub {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_stub {</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
 <span><span class="co">#&gt;   font-size: 100%;</span></span>
@@ -441,7 +441,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   padding-right: 5px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_stub_row_group {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_stub_row_group {</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
 <span><span class="co">#&gt;   font-size: 100%;</span></span>
@@ -455,11 +455,11 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   vertical-align: top;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_row_group_first td {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_row_group_first td {</span></span>
 <span><span class="co">#&gt;   border-top-width: 2px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_summary_row {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_summary_row {</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
 <span><span class="co">#&gt;   text-transform: inherit;</span></span>
@@ -469,16 +469,16 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   padding-right: 5px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_first_summary_row {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_first_summary_row {</span></span>
 <span><span class="co">#&gt;   border-top-style: solid;</span></span>
 <span><span class="co">#&gt;   border-top-color: #D3D3D3;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_first_summary_row.thick {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_first_summary_row.thick {</span></span>
 <span><span class="co">#&gt;   border-top-width: 2px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_last_summary_row {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_last_summary_row {</span></span>
 <span><span class="co">#&gt;   padding-top: 8px;</span></span>
 <span><span class="co">#&gt;   padding-bottom: 8px;</span></span>
 <span><span class="co">#&gt;   padding-left: 5px;</span></span>
@@ -488,7 +488,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   border-bottom-color: #D3D3D3;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_grand_summary_row {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_grand_summary_row {</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
 <span><span class="co">#&gt;   text-transform: inherit;</span></span>
@@ -498,7 +498,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   padding-right: 5px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_first_grand_summary_row {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_first_grand_summary_row {</span></span>
 <span><span class="co">#&gt;   padding-top: 8px;</span></span>
 <span><span class="co">#&gt;   padding-bottom: 8px;</span></span>
 <span><span class="co">#&gt;   padding-left: 5px;</span></span>
@@ -508,11 +508,11 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   border-top-color: #D3D3D3;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_striped {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_striped {</span></span>
 <span><span class="co">#&gt;   background-color: rgba(128, 128, 128, 0.05);</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_table_body {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_table_body {</span></span>
 <span><span class="co">#&gt;   border-top-style: solid;</span></span>
 <span><span class="co">#&gt;   border-top-width: 2px;</span></span>
 <span><span class="co">#&gt;   border-top-color: #D3D3D3;</span></span>
@@ -521,7 +521,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   border-bottom-color: #D3D3D3;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_footnotes {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_footnotes {</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
 <span><span class="co">#&gt;   border-bottom-style: none;</span></span>
@@ -535,7 +535,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   border-right-color: #D3D3D3;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_footnote {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_footnote {</span></span>
 <span><span class="co">#&gt;   margin: 0px;</span></span>
 <span><span class="co">#&gt;   font-size: 90%;</span></span>
 <span><span class="co">#&gt;   padding-left: 4px;</span></span>
@@ -544,7 +544,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   padding-right: 5px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_sourcenotes {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_sourcenotes {</span></span>
 <span><span class="co">#&gt;   color: #333333;</span></span>
 <span><span class="co">#&gt;   background-color: #FFFFFF;</span></span>
 <span><span class="co">#&gt;   border-bottom-style: none;</span></span>
@@ -558,7 +558,7 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   border-right-color: #D3D3D3;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_sourcenote {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_sourcenote {</span></span>
 <span><span class="co">#&gt;   font-size: 90%;</span></span>
 <span><span class="co">#&gt;   padding-top: 4px;</span></span>
 <span><span class="co">#&gt;   padding-bottom: 4px;</span></span>
@@ -566,64 +566,64 @@ model plot (with <code><a href="../reference/ci_plot.html">stRoke::ci_plot()</a>
 <span><span class="co">#&gt;   padding-right: 5px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_left {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_left {</span></span>
 <span><span class="co">#&gt;   text-align: left;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_center {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_center {</span></span>
 <span><span class="co">#&gt;   text-align: center;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_right {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_right {</span></span>
 <span><span class="co">#&gt;   text-align: right;</span></span>
 <span><span class="co">#&gt;   font-variant-numeric: tabular-nums;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_font_normal {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_font_normal {</span></span>
 <span><span class="co">#&gt;   font-weight: normal;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_font_bold {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_font_bold {</span></span>
 <span><span class="co">#&gt;   font-weight: bold;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_font_italic {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_font_italic {</span></span>
 <span><span class="co">#&gt;   font-style: italic;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_super {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_super {</span></span>
 <span><span class="co">#&gt;   font-size: 65%;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_footnote_marks {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_footnote_marks {</span></span>
 <span><span class="co">#&gt;   font-style: italic;</span></span>
 <span><span class="co">#&gt;   font-weight: normal;</span></span>
 <span><span class="co">#&gt;   font-size: 75%;</span></span>
 <span><span class="co">#&gt;   vertical-align: 0.4em;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_asterisk {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_asterisk {</span></span>
 <span><span class="co">#&gt;   font-size: 100%;</span></span>
 <span><span class="co">#&gt;   vertical-align: 0;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_indent_1 {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_indent_1 {</span></span>
 <span><span class="co">#&gt;   text-indent: 5px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_indent_2 {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_indent_2 {</span></span>
 <span><span class="co">#&gt;   text-indent: 10px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_indent_3 {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_indent_3 {</span></span>
 <span><span class="co">#&gt;   text-indent: 15px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_indent_4 {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_indent_4 {</span></span>
 <span><span class="co">#&gt;   text-indent: 20px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; #zlonxkjxpy .gt_indent_5 {</span></span>
+<span><span class="co">#&gt; #fzlccdqrrt .gt_indent_5 {</span></span>
 <span><span class="co">#&gt;   text-indent: 25px;</span></span>
 <span><span class="co">#&gt; }</span></span>
 <span><span class="co">#&gt; &lt;/style&gt;</span></span>

docs/articles/ds2dd.html

@@ -145,10 +145,10 @@ Handbook”</a> more is written on interfacing with REDCap in R using the
 <h3 id="step-4---data-upload">Step 4 - Data upload<a class="anchor" aria-label="anchor" href="#step-4---data-upload"></a>
 </h3>
 <p>The same two options are available for data upload as meta data
-upload: manual og through <code>REDCapR</code>.</p>
+upload: manual or through <code>REDCapR</code>.</p>
 <p>Only the latter is shown here.</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="co"># new column nams are applied</span></span>
+<code class="sourceCode R"><span><span class="co"># new column names are applied</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">datadictionary</span><span class="op">$</span><span class="va">`Column names`</span></span>
 <span></span>
 <span><span class="fu">REDCapR</span><span class="fu">::</span><span class="fu"><a href="https://ouhscbbmc.github.io/REDCapR/reference/redcap_write.html" class="external-link">redcap_write</a></span><span class="op">(</span></span>

docs/index.html

@@ -140,7 +140,7 @@
 <li><a href="https://doi.org/10.5281/zenodo.7572023" class="external-link"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.7572023.svg" alt="DOI"></a></li>
 <li><a href="https://github.com/agdamsbo/stRoke/actions/workflows/R-CMD-check.yaml" class="external-link"><img src="https://github.com/agdamsbo/stRoke/actions/workflows/R-CMD-check.yaml/badge.svg" alt="Github Actions"></a></li>
 <li><a href="https://github.com/agdamsbo/stRoke/actions/workflows/pages/pages-build-deployment" class="external-link"><img src="https://github.com/agdamsbo/stRoke/actions/workflows/pages/pages-build-deployment/badge.svg" alt="Page deployed"></a></li>
-<li><a href="https://codecov.io/github/agdamsbo/stRoke" class="external-link"><img src="https://codecov.io/github/agdamsbo/stRoke/branch/main/graph/badge.svg?token=U0RBZYSKG5" alt="codecov"></a></li>
+<li><a href="https://app.codecov.io/gh/agdamsbo/stRoke?branch=main" class="external-link"><img src="https://codecov.io/gh/agdamsbo/stRoke/branch/main/graph/badge.svg" alt="Codecov test coverage"></a></li>
 <li><a href="https://cran.r-project.org/package=stRoke" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/stRoke" alt="CRAN downloads"></a></li>
 </ul>
 </div>

docs/pkgdown.yml

@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   ds2dd: ds2dd.html
   toolbox: toolbox.html
-last_built: 2023-04-13T05:56Z
+last_built: 2023-04-13T09:12Z
 

docs/reference/label_select.html

@@ -94,15 +94,15 @@ Alternative is to use attributes, eg from <code><a href="https://hbiostat.org/R/
 <span class="r-in"><span><span class="fu">label_select</span><span class="op">(</span><span class="va">labels_all</span>,<span class="va">vars</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> hypertension ~ "Known hypertension"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x7ff03334c010&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x7fb2db2ca250&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[2]]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> diabetes ~ "Known diabetes"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x7ff03334c010&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x7fb2db2ca250&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [[3]]</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> mrs_1 ~ "One month mRS"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x7ff03334c010&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x7fb2db2ca250&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## With gtsummary::tbl_summary()</span></span></span>

docs/reference/quantile_cut.html

@@ -120,8 +120,8 @@ as borders in case of y!=NULL.</p></dd>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fl">1</span><span class="op">:</span><span class="fl">450</span></span></span>
 <span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fl">6</span><span class="op">:</span><span class="fl">750</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu">quantile_cut</span><span class="op">(</span><span class="va">aa</span>,groups<span class="op">=</span><span class="fl">4</span>,detail.list<span class="op">=</span><span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span> <span class="co">## Cuts quartiles</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>     [1,259]   (259,514]   (514,753] (753,1e+03] </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     [2,253]   (253,497]   (497,744] (744,1e+03] </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>         500         502         499         499 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>         501         500         500         499 </span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

inst/WORDLIST

@@ -1,7 +1,9 @@
 Andreas
 Changelog
+Codecov
 DDMMYY
 DOI
+DataDictionary
 Gammelgaard
 Github
 Kraglund
@@ -10,6 +12,7 @@ NA's
 OLR
 ORCID
 OpenAI's
+REDCap
 REDCapRITS
 RStudio
 Randomisation
@@ -25,6 +28,7 @@ al
 annonymized
 bstfun
 calc
+characterstrings
 chatgpt
 christophergandrud
 ci
@@ -39,6 +43,7 @@ ddmmyyxxxx
 difftime
 dk
 doi
+ds
 eeptools
 eg
 et
@@ -63,6 +68,7 @@ lm
 lst
 luminance
 mRS
+og
 olr
 recognised
 rgb

vignettes/ds2dd.Rmd

@@ -70,12 +70,12 @@ In the ["REDCap R Handbook"](https://agdamsbo.github.io/redcap-r-handbook/) more
 
 ## Step 4 - Data upload
 
-The same two options are available for data upload as meta data upload: manual og through `REDCapR`.
+The same two options are available for data upload as meta data upload: manual or through `REDCapR`.
 
 Only the latter is shown here.
 
 ```{r eval=FALSE}
-# new column nams are applied
+# new column names are applied
 colnames(ds) <- datadictionary$`Column names`
 
 REDCapR::redcap_write(