diff --git a/404.html b/404.html
index 57675e0..07dc53d 100644
--- a/404.html
+++ b/404.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="https://agdamsbo.github.io/freesearcheR/index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index b7cff41..2ef70e0 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index a7072ec..3de8d0c 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/QA.html b/QA.html
index 7a490a0..a337863 100644
--- a/QA.html
+++ b/QA.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/ROADMAP.html b/ROADMAP.html
index 8e1bb06..16c802b 100644
--- a/ROADMAP.html
+++ b/ROADMAP.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index c834ed1..debd8d4 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -48,13 +48,13 @@
 
       <p>Damsbo A (2025).
 <em>freesearcheR: Browser Based Data Analysis</em>.
-R package version 25.2.1, https://agdamsbo.github.io/freesearcheR/, <a href="https://github.com/agdamsbo/freesearcheR" class="external-link">https://github.com/agdamsbo/freesearcheR</a>.
+R package version 25.3.1, https://agdamsbo.github.io/freesearcheR/, <a href="https://github.com/agdamsbo/freesearcheR" class="external-link">https://github.com/agdamsbo/freesearcheR</a>.
 </p>
       <pre>@Manual{,
   title = {freesearcheR: Browser Based Data Analysis},
   author = {Andreas Gammelgaard Damsbo},
   year = {2025},
-  note = {R package version 25.2.1, https://agdamsbo.github.io/freesearcheR/},
+  note = {R package version 25.3.1, https://agdamsbo.github.io/freesearcheR/},
   url = {https://github.com/agdamsbo/freesearcheR},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index edf37f0..5442747 100644
--- a/index.html
+++ b/index.html
@@ -25,7 +25,7 @@
 
     <a class="navbar-brand me-2" href="index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index cb41040..94ecdc4 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,15 +35,21 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="25.2.1" id="freesearcher-2521">freesearcheR 25.2.1<a class="anchor" aria-label="anchor" href="#freesearcher-2521"></a></h2>
+<h2 class="pkg-version" data-toc-text="25.3.1" id="freesearcher-2531">freesearcheR 25.3.1<a class="anchor" aria-label="anchor" href="#freesearcher-2531"></a></h2>
 <p>First steps towards a more focused and simplified interface.</p>
 <p>Focus will be on ease of use, handling basic functionality for data inspection and descriptive analyses.</p>
 <p>Inspired by the Stroke Center implementation guidelines of the WSO, we will apply a similar approach to this project in order to keep the interface simple and robust. Basic functions for descriptive analyses and data browsing are the basics. More advanced features like regression analyses are added for learning purposes, but really should be done by one self in software like <em>R</em> to ensure learning and reproducibility.</p>
 <p>Teal dependencies removed. The teal framework really seems very powerful and promising, but it will also mean less control and more clutter. May come up again later.</p>
-<p>All main components have been implemented.</p>
-<p>Next steps are:</p>
+<p>All main components have been implemented:</p>
+<ul><li><p>Data import from different sources</p></li>
+<li><p>Data management (variable creation, re-classing, naming, labelling and more)</p></li>
+<li><p>Basic data comparisons and descriptive analyses</p></li>
+<li><p>Basic data visualisations with a select set of plot types great for publication purposes</p></li>
+<li><p>Regression analysis of basic clinical cross-sectional data (mixed models of repeated measures and survival analyses is on the table)</p></li>
+<li><p>Export of outputs (descriptive analyses and regression) as well as modified dataset (code is also showed, but not working as it should)</p></li>
+</ul><p>Next steps are:</p>
 <ul><li><p>Polished code export</p></li>
-<li><p>Improved workflow and thorough step-wise guide/documentation</p></li>
+<li><p>Improved workflow and descriptive text as well as thorough step-wise guide/documentation (possibly with small videos)</p></li>
 <li><p>Implement in clinical projects</p></li>
 <li><p>Implement in data analysis courses</p></li>
 <li><p>Extensive testing and bug squashing</p></li>
diff --git a/pkgdown.yml b/pkgdown.yml
index 513a824..d21596b 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2025-03-05T20:46Z
+last_built: 2025-03-06T07:23Z
 urls:
   reference: https://agdamsbo.github.io/freesearcheR/reference
   article: https://agdamsbo.github.io/freesearcheR/articles
diff --git a/reference/add_class_icon.html b/reference/add_class_icon.html
index f24026e..725e512 100644
--- a/reference/add_class_icon.html
+++ b/reference/add_class_icon.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_sparkline.html b/reference/add_sparkline.html
index 7c15395..d30fcfb 100644
--- a/reference/add_sparkline.html
+++ b/reference/add_sparkline.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/all_but.html b/reference/all_but.html
index 348857f..c44f8c6 100644
--- a/reference/all_but.html
+++ b/reference/all_but.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/append_list.html b/reference/append_list.html
index e5084a3..829c488 100644
--- a/reference/append_list.html
+++ b/reference/append_list.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/argsstring2list.html b/reference/argsstring2list.html
index a7ec0ac..8cece7f 100644
--- a/reference/argsstring2list.html
+++ b/reference/argsstring2list.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/baseline_table.html b/reference/baseline_table.html
index 4c4099a..c4e3c06 100644
--- a/reference/baseline_table.html
+++ b/reference/baseline_table.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/clean_date.html b/reference/clean_date.html
index 23eefe3..2ee9244 100644
--- a/reference/clean_date.html
+++ b/reference/clean_date.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/clean_sep.html b/reference/clean_sep.html
index 5cb9546..6824ba6 100644
--- a/reference/clean_sep.html
+++ b/reference/clean_sep.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/columnSelectInput.html b/reference/columnSelectInput.html
index 7b11f7d..7979d24 100644
--- a/reference/columnSelectInput.html
+++ b/reference/columnSelectInput.html
@@ -9,7 +9,7 @@ Adds the option to select "none" which is handled later'></head><body>
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/contrast_text.html b/reference/contrast_text.html
index 0dd7ba0..f67a80f 100644
--- a/reference/contrast_text.html
+++ b/reference/contrast_text.html
@@ -9,7 +9,7 @@ background color."></head><body>
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/create_overview_datagrid.html b/reference/create_overview_datagrid.html
index 6c1cab8..c6bb874 100644
--- a/reference/create_overview_datagrid.html
+++ b/reference/create_overview_datagrid.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/custom_theme.html b/reference/custom_theme.html
index c469109..8fc746d 100644
--- a/reference/custom_theme.html
+++ b/reference/custom_theme.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cut-variable.html b/reference/cut-variable.html
index 8312a69..3a18e5c 100644
--- a/reference/cut-variable.html
+++ b/reference/cut-variable.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cut.html b/reference/cut.html
index 51e8316..64fbc9b 100644
--- a/reference/cut.html
+++ b/reference/cut.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/data-correlations.html b/reference/data-correlations.html
index 1b7d500..5e744cd 100644
--- a/reference/data-correlations.html
+++ b/reference/data-correlations.html
@@ -9,7 +9,7 @@ Data correlations evaluation module"></head><body>
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/data-plots.html b/reference/data-plots.html
index a97af7a..a84e817 100644
--- a/reference/data-plots.html
+++ b/reference/data-plots.html
@@ -17,7 +17,7 @@ Beautiful sankey plot with option to split by a tertiary group"></head><body>
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/data-summary.html b/reference/data-summary.html
index 7b5020c..cee3c29 100644
--- a/reference/data-summary.html
+++ b/reference/data-summary.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/default_format_arguments.html b/reference/default_format_arguments.html
index 03c075b..c61ccda 100644
--- a/reference/default_format_arguments.html
+++ b/reference/default_format_arguments.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/default_parsing.html b/reference/default_parsing.html
index 06b8b55..757aa6b 100644
--- a/reference/default_parsing.html
+++ b/reference/default_parsing.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/factorize.html b/reference/factorize.html
index fc205e4..f0ffbb6 100644
--- a/reference/factorize.html
+++ b/reference/factorize.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/file_export.html b/reference/file_export.html
index 6adaeef..c678ed8 100644
--- a/reference/file_export.html
+++ b/reference/file_export.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/format_writer.html b/reference/format_writer.html
index ede0c82..d5a0618 100644
--- a/reference/format_writer.html
+++ b/reference/format_writer.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_fun_options.html b/reference/get_fun_options.html
index 5841170..3bedca9 100644
--- a/reference/get_fun_options.html
+++ b/reference/get_fun_options.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_label.html b/reference/get_label.html
index 1fe177f..e2a8ea5 100644
--- a/reference/get_label.html
+++ b/reference/get_label.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_plot_options.html b/reference/get_plot_options.html
index 2be1943..95867b3 100644
--- a/reference/get_plot_options.html
+++ b/reference/get_plot_options.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getfun.html b/reference/getfun.html
index 9c12d8c..82e0a0d 100644
--- a/reference/getfun.html
+++ b/reference/getfun.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -132,7 +132,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span>         z$qr &lt;- NULL</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>     z</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x564b9a27c918&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x556a34cd2538&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: namespace:stats&gt;</span>
 </code></pre></div>
     </div>
diff --git a/reference/gg_theme_export.html b/reference/gg_theme_export.html
index 9c0e915..5a63f6a 100644
--- a/reference/gg_theme_export.html
+++ b/reference/gg_theme_export.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/gg_theme_shiny.html b/reference/gg_theme_shiny.html
index ba15f38..8fb1981 100644
--- a/reference/gg_theme_shiny.html
+++ b/reference/gg_theme_shiny.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 10cfbab..5b1d4df 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index_embed.html b/reference/index_embed.html
index f964bf3..1c1411f 100644
--- a/reference/index_embed.html
+++ b/reference/index_embed.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/is_any_class.html b/reference/is_any_class.html
index 1a4d541..5e4f680 100644
--- a/reference/is_any_class.html
+++ b/reference/is_any_class.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/is_consecutive.html b/reference/is_consecutive.html
index 125cf4f..d09f951 100644
--- a/reference/is_consecutive.html
+++ b/reference/is_consecutive.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/is_datetime.html b/reference/is_datetime.html
index aa4cad0..d236c58 100644
--- a/reference/is_datetime.html
+++ b/reference/is_datetime.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/is_valid_redcap_url.html b/reference/is_valid_redcap_url.html
index 0f775d5..139b0f0 100644
--- a/reference/is_valid_redcap_url.html
+++ b/reference/is_valid_redcap_url.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/is_valid_token.html b/reference/is_valid_token.html
index 8641aaa..4bbd19b 100644
--- a/reference/is_valid_token.html
+++ b/reference/is_valid_token.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/launch_freesearcheR.html b/reference/launch_freesearcheR.html
index f8af665..1a1fe85 100644
--- a/reference/launch_freesearcheR.html
+++ b/reference/launch_freesearcheR.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/line_break.html b/reference/line_break.html
index 6b60734..150ca1f 100644
--- a/reference/line_break.html
+++ b/reference/line_break.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/m_datafileUI.html b/reference/m_datafileUI.html
index ea22c69..b996612 100644
--- a/reference/m_datafileUI.html
+++ b/reference/m_datafileUI.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/merge_long.html b/reference/merge_long.html
index b599ef5..57fed7c 100644
--- a/reference/merge_long.html
+++ b/reference/merge_long.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/modify_qmd.html b/reference/modify_qmd.html
index 4fb896f..05f2c53 100644
--- a/reference/modify_qmd.html
+++ b/reference/modify_qmd.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/outcome_type.html b/reference/outcome_type.html
index 91052a3..8a748f9 100644
--- a/reference/outcome_type.html
+++ b/reference/outcome_type.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/overview_vars.html b/reference/overview_vars.html
index 2e939ac..58bb4e2 100644
--- a/reference/overview_vars.html
+++ b/reference/overview_vars.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/plot.tbl_regression.html b/reference/plot.tbl_regression.html
index 169c4c5..271e39c 100644
--- a/reference/plot.tbl_regression.html
+++ b/reference/plot.tbl_regression.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/plot_sankey_single.html b/reference/plot_sankey_single.html
index 866b0e2..97bb8ac 100644
--- a/reference/plot_sankey_single.html
+++ b/reference/plot_sankey_single.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/possible_functions.html b/reference/possible_functions.html
index 7256086..aab3e32 100644
--- a/reference/possible_functions.html
+++ b/reference/possible_functions.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/possible_plots.html b/reference/possible_plots.html
index 909e96f..aa6683b 100644
--- a/reference/possible_plots.html
+++ b/reference/possible_plots.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/read_input.html b/reference/read_input.html
index 62770c6..4e34f3b 100644
--- a/reference/read_input.html
+++ b/reference/read_input.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/redcap_read_shiny_module.html b/reference/redcap_read_shiny_module.html
index 493cb77..758564a 100644
--- a/reference/redcap_read_shiny_module.html
+++ b/reference/redcap_read_shiny_module.html
@@ -9,7 +9,7 @@ Test app for the redcap_read_shiny_module"></head><body>
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/regression_model.html b/reference/regression_model.html
index 9a16488..e4c134f 100644
--- a/reference/regression_model.html
+++ b/reference/regression_model.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/regression_table.html b/reference/regression_table.html
index d035797..85f1ed0 100644
--- a/reference/regression_table.html
+++ b/reference/regression_table.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/remove_empty_cols.html b/reference/remove_empty_cols.html
index 8f6da42..8a2ae5c 100644
--- a/reference/remove_empty_cols.html
+++ b/reference/remove_empty_cols.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/remove_na_attr.html b/reference/remove_na_attr.html
index 017ea42..077f6e3 100644
--- a/reference/remove_na_attr.html
+++ b/reference/remove_na_attr.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/sankey_ready.html b/reference/sankey_ready.html
index 2d6e4aa..4d639a1 100644
--- a/reference/sankey_ready.html
+++ b/reference/sankey_ready.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/shiny_freesearcheR.html b/reference/shiny_freesearcheR.html
index e983a5d..10d1824 100644
--- a/reference/shiny_freesearcheR.html
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@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/specify_qmd_format.html b/reference/specify_qmd_format.html
index 542c701..a61a4be 100644
--- a/reference/specify_qmd_format.html
+++ b/reference/specify_qmd_format.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/subset_types.html b/reference/subset_types.html
index 68733a9..47b1ba5 100644
--- a/reference/subset_types.html
+++ b/reference/subset_types.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/supported_functions.html b/reference/supported_functions.html
index 60c4422..9b952f3 100644
--- a/reference/supported_functions.html
+++ b/reference/supported_functions.html
@@ -9,7 +9,7 @@ unique for each element on list.'></head><body>
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/supported_plots.html b/reference/supported_plots.html
index 9c0b79d..a254124 100644
--- a/reference/supported_plots.html
+++ b/reference/supported_plots.html
@@ -23,7 +23,7 @@ tertiary.type: Tertiary variable data type (continuous, dichotomous or ordinal)
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/tbl_merge.html b/reference/tbl_merge.html
index 7cbcd52..ce185e3 100644
--- a/reference/tbl_merge.html
+++ b/reference/tbl_merge.html
@@ -9,7 +9,7 @@ spanner names."></head><body>
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/update-factor.html b/reference/update-factor.html
index 3d2cdb0..a9d901d 100644
--- a/reference/update-factor.html
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@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/update-variables.html b/reference/update-variables.html
index 10496b8..5d9db98 100644
--- a/reference/update-variables.html
+++ b/reference/update-variables.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/update_variables_datagrid.html b/reference/update_variables_datagrid.html
index 814e52f..07a77d1 100644
--- a/reference/update_variables_datagrid.html
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@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">freesearcheR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/vertical_stacked_bars.html b/reference/vertical_stacked_bars.html
index 5486dce..5ad3117 100644
--- a/reference/vertical_stacked_bars.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/write_quarto.html b/reference/write_quarto.html
index b264639..30a7602 100644
--- a/reference/write_quarto.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.2.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">25.3.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index dfb0b8e..427bff3 100644
--- a/search.json
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Notwithstanding provision License, material add covered work, may (authorized copyright holders material) supplement terms License terms: Disclaiming warranty limiting liability differently terms sections 15 16 License; Requiring preservation specified reasonable legal notices author attributions material Appropriate Legal Notices displayed works containing ; Prohibiting misrepresentation origin material, requiring modified versions material marked reasonable ways different original version; Limiting use publicity purposes names licensors authors material; Declining grant rights trademark law use trade names, trademarks, service marks; Requiring indemnification licensors authors material anyone conveys material (modified versions ) contractual assumptions liability recipient, liability contractual assumptions directly impose licensors authors. non-permissive additional terms considered “restrictions” within meaning section 10. Program received , part , contains notice stating governed License along term restriction, may remove term. license document contains restriction permits relicensing conveying License, may add covered work material governed terms license document, provided restriction survive relicensing conveying. add terms covered work accord section, must place, relevant source files, statement additional terms apply files, notice indicating find applicable terms. Additional terms, permissive non-permissive, may stated form separately written license, stated exceptions; requirements apply either way.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_8-termination","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"8. Termination.","title":"GNU Affero General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. Termination rights section terminate licenses parties received copies rights License. rights terminated permanently reinstated, qualify receive new licenses material section 10.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_9-acceptance-not-required-for-having-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"9. Acceptance Not Required for Having Copies.","title":"GNU Affero General Public License","text":"required accept License order receive run copy Program. Ancillary propagation covered work occurring solely consequence using peer--peer transmission receive copy likewise require acceptance. However, nothing License grants permission propagate modify covered work. actions infringe copyright accept License. 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Automatic Licensing of Downstream Recipients.","title":"GNU Affero General Public License","text":"time convey covered work, recipient automatically receives license original licensors, run, modify propagate work, subject License. responsible enforcing compliance third parties License. “entity transaction” transaction transferring control organization, substantially assets one, subdividing organization, merging organizations. propagation covered work results entity transaction, party transaction receives copy work also receives whatever licenses work party’s predecessor interest give previous paragraph, plus right possession Corresponding Source work predecessor interest, predecessor can get reasonable efforts. may impose restrictions exercise rights granted affirmed License. example, may impose license fee, royalty, charge exercise rights granted License, may initiate litigation (including cross-claim counterclaim lawsuit) alleging patent claim infringed making, using, selling, offering sale, importing Program portion .","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_11-patents","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"11. Patents.","title":"GNU Affero General Public License","text":"“contributor” copyright holder authorizes use License Program work Program based. work thus licensed called contributor’s “contributor version”. contributor’s “essential patent claims” patent claims owned controlled contributor, whether already acquired hereafter acquired, infringed manner, permitted License, making, using, selling contributor version, include claims infringed consequence modification contributor version. purposes definition, “control” includes right grant patent sublicenses manner consistent requirements License. contributor grants non-exclusive, worldwide, royalty-free patent license contributor’s essential patent claims, make, use, sell, offer sale, import otherwise run, modify propagate contents contributor version. following three paragraphs, “patent license” express agreement commitment, however denominated, enforce patent (express permission practice patent covenant sue patent infringement). “grant” patent license party means make agreement commitment enforce patent party. convey covered work, knowingly relying patent license, Corresponding Source work available anyone copy, free charge terms License, publicly available network server readily accessible means, must either (1) cause Corresponding Source available, (2) arrange deprive benefit patent license particular work, (3) arrange, manner consistent requirements License, extend patent license downstream recipients. “Knowingly relying” means actual knowledge , patent license, conveying covered work country, recipient’s use covered work country, infringe one identifiable patents country reason believe valid. , pursuant connection single transaction arrangement, convey, propagate procuring conveyance , covered work, grant patent license parties receiving covered work authorizing use, propagate, modify convey specific copy covered work, patent license grant automatically extended recipients covered work works based . patent license “discriminatory” include within scope coverage, prohibits exercise , conditioned non-exercise one rights specifically granted License. may convey covered work party arrangement third party business distributing software, make payment third party based extent activity conveying work, third party grants, parties receive covered work , discriminatory patent license () connection copies covered work conveyed (copies made copies), (b) primarily connection specific products compilations contain covered work, unless entered arrangement, patent license granted, prior 28 March 2007. 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Remote Network Interaction; Use with the GNU General Public License.","title":"GNU Affero General Public License","text":"Notwithstanding provision License, modify Program, modified version must prominently offer users interacting remotely computer network (version supports interaction) opportunity receive Corresponding Source version providing access Corresponding Source network server charge, standard customary means facilitating copying software. Corresponding Source shall include Corresponding Source work covered version 3 GNU General Public License incorporated pursuant following paragraph. Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU General Public License single combined work, convey resulting work. terms License continue apply part covered work, work combined remain governed version 3 GNU General Public License.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License.","title":"GNU Affero General Public License","text":"Free Software Foundation may publish revised /new versions GNU Affero General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU Affero General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU Affero General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU Affero General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty.","title":"GNU Affero General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability.","title":"GNU Affero General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16.","title":"GNU Affero General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU Affero General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. software can interact users remotely computer network, also make sure provides way users get source. example, program web application, interface display “Source” link leads users archive code. many ways offer source, different solutions better different programs; see section 13 specific requirements. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU AGPL, see https://www.gnu.org/licenses/.","code":"<one line to give the program's name and a brief idea of what it does.>     Copyright (C) <year>  <name of author>      This program is free software: you can redistribute it and/or modify     it under the terms of the GNU Affero General Public License as     published by the Free Software Foundation, either version 3 of the     License, or (at your option) any later version.      This program is distributed in the hope that it will be useful,     but WITHOUT ANY WARRANTY; without even the implied warranty of     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the     GNU Affero General Public License for more details.      You should have received a copy of the GNU Affero General Public License     along with this program.  If not, see <https://www.gnu.org/licenses/>."},{"path":"https://agdamsbo.github.io/freesearcheR/QA.html","id":null,"dir":"","previous_headings":"","what":"Questions and answers","title":"Questions and answers","text":"complete instructions set available, collection questions answers project use app.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/QA.html","id":"are-you-keeping-the-uploaded-data","dir":"","previous_headings":"","what":"Are you keeping the uploaded data?","title":"Questions and answers","text":"! uploaded data deleted session ends, stored analyses immediately deleted.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/ROADMAP.html","id":null,"dir":"","previous_headings":"","what":"Project roadmap","title":"Project roadmap","text":"current state app considered experimental, lot things still changing. , however, usable state, basic functions available user. (actual list quite long growing) planned features improvements: Stratified analyses Additional study designs: Cross-sectional data analyses Longitudinal data analyses Survival analysis detailed variable browser Add histograms data distribution. 2025-01-16 Option edit labels. 2025-01-16 output controls Theming output tables Select analyses include report Export modified data. 2025-01-16 Include reproducible code steps (maybe , steps, final dataset can exported) Modify factor levels Factor level modifications possible converting factors numeric > cutting numeric desired fixed values. 2024-12-12 options date/datetime/time grouping/factoring. Included weekday month-options. 2024-12-12 Graphs plots Correlation matrix plot data exploration 2025-2-20 Grotta bars ordianl outcomes Coefficient plotting regression analyses (forest plot) 2025-2-20","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andreas Gammelgaard Damsbo. Author, maintainer.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo (2025). freesearcheR: Browser Based Data Analysis. R package version 25.2.1, https://agdamsbo.github.io/freesearcheR/, https://github.com/agdamsbo/freesearcheR.","code":"@Manual{,   title = {freesearcheR: Browser Based Data Analysis},   author = {Andreas Gammelgaard Damsbo},   year = {2025},   note = {R package version 25.2.1, https://agdamsbo.github.io/freesearcheR/},   url = {https://github.com/agdamsbo/freesearcheR}, }"},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"freesearcher","dir":"","previous_headings":"","what":"Browser Based Data Analysis","title":"Browser Based Data Analysis","text":"package backbone freesearcheR, free open-source browser based data exploration analysis tool clinicians researchers publication ready output. package freesearcheR-tool part larger initiative democratize health data analysis remove barriers clinicians engage health research. freesearcheR-tool online accessible : link app freely hosted shinyapps.io. feedback welcome can shared GitHub issue. Initiatives funding continued development tool surrounding initiatives ongoing.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"install-locally","dir":"","previous_headings":"","what":"Install locally","title":"Browser Based Data Analysis","text":"freesearcheR-tool can also launched locally. data.frame available global environment accessible interface.","code":"require(\"devtools\") devtools::install_github(\"agdamsbo/freesearcheR\") library(freesearcheR) # By loading mtcars to the environment, it will be available # in the interface like any other data.frame data(mtcars) shiny_freesearcheR()"},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Browser Based Data Analysis","text":"Please note freesearcheR project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert class grid column to icon — add_class_icon","title":"Convert class grid column to icon — add_class_icon","text":"Convert class grid column icon","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert class grid column to icon — add_class_icon","text":"","code":"add_class_icon(grid, column = \"class\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert class grid column to icon — add_class_icon","text":"grid grid column column","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert class grid column to icon — add_class_icon","text":"datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert class grid column to icon — add_class_icon","text":"","code":"mtcars |>   overview_vars() |>   toastui::datagrid() |>   add_class_icon()      {\"x\":{\"nrow\":11,\"ncol\":7,\"data\":[[\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\"],[\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\"],[\"mpg\",\"cyl\",\"disp\",\"hp\",\"drat\",\"wt\",\"qsec\",\"vs\",\"am\",\"gear\",\"carb\"],[0,0,0,0,0,0,0,0,0,0,0],[1,1,1,1,1,1,1,1,1,1,1],[25,3,27,22,22,29,30,2,2,3,6],[[21,21,22.8,21.4,18.7,18.1,14.3,24.4,22.8,19.2,17.8,16.4,17.3,15.2,10.4,10.4,14.7,32.4,30.4,33.9,21.5,15.5,15.2,13.3,19.2,27.3,26,30.4,15.8,19.7,15,21.4],[6,6,4,6,8,6,8,4,4,6,6,8,8,8,8,8,8,4,4,4,4,8,8,8,8,4,4,4,8,6,8,4],[160,160,108,258,360,225,360,146.7,140.8,167.6,167.6,275.8,275.8,275.8,472,460,440,78.7,75.7,71.09999999999999,120.1,318,304,350,400,79,120.3,95.09999999999999,351,145,301,121],[110,110,93,110,175,105,245,62,95,123,123,180,180,180,205,215,230,66,52,65,97,150,150,245,175,66,91,113,264,175,335,109],[3.9,3.9,3.85,3.08,3.15,2.76,3.21,3.69,3.92,3.92,3.92,3.07,3.07,3.07,2.93,3,3.23,4.08,4.93,4.22,3.7,2.76,3.15,3.73,3.08,4.08,4.43,3.77,4.22,3.62,3.54,4.11],[2.62,2.875,2.32,3.215,3.44,3.46,3.57,3.19,3.15,3.44,3.44,4.07,3.73,3.78,5.25,5.424,5.345,2.2,1.615,1.835,2.465,3.52,3.435,3.84,3.845,1.935,2.14,1.513,3.17,2.77,3.57,2.78],[16.46,17.02,18.61,19.44,17.02,20.22,15.84,20,22.9,18.3,18.9,17.4,17.6,18,17.98,17.82,17.42,19.47,18.52,19.9,20.01,16.87,17.3,15.41,17.05,18.9,16.7,16.9,14.5,15.5,14.6,18.6],[0,0,1,1,0,1,0,1,1,1,1,0,0,0,0,0,0,1,1,1,1,0,0,0,0,1,0,1,0,0,0,1],[1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1,1,1],[4,4,4,3,3,3,3,4,4,4,4,3,3,3,3,3,3,4,4,4,3,3,3,3,3,4,5,5,5,5,5,4],[4,4,1,1,2,1,4,2,2,4,4,3,3,3,4,4,4,1,2,1,1,2,2,4,2,1,2,2,4,6,8,2]]],\"colnames\":[\"class\",\"type\",\"name\",\"n_missing\",\"p_complete\",\"n_unique\",\"vals\"],\"options\":{\"columns\":[{\"header\":\"class\",\"name\":\"class\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"},\"type\":\"datagrid.renderer.format\",\"options\":{\"formatted\":[\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\"]}},\"width\":60},{\"header\":\"type\",\"name\":\"type\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"name\",\"name\":\"name\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"n_missing\",\"name\":\"n_missing\",\"sortable\":true,\"align\":\"right\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"p_complete\",\"name\":\"p_complete\",\"sortable\":true,\"align\":\"right\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"n_unique\",\"name\":\"n_unique\",\"sortable\":true,\"align\":\"right\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"vals\",\"name\":\"vals\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}}],\"bodyHeight\":\"fitToParent\",\"draggable\":false,\"usageStatistics\":false,\"contextMenu\":null,\"rowHeight\":\"auto\"},\"theme\":\"clean\",\"themeOptions\":{\"cell\":{\"normal\":{\"showHorizontalBorder\":true}}},\"language\":\"en\",\"languageOptions\":[],\"filters\":false,\"rowAttributes\":[],\"validationInput\":false,\"dataAsInput\":false,\"dragInput\":false},\"evals\":[\"options.columns.0.renderer.type\"],\"jsHooks\":[]}"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_sparkline.html","id":null,"dir":"Reference","previous_headings":"","what":"Add sparkline to datagrid — add_sparkline","title":"Add sparkline to datagrid — add_sparkline","text":"Add sparkline datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_sparkline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add sparkline to datagrid — add_sparkline","text":"","code":"add_sparkline(   grid,   column = \"vals\",   color.main = \"#2a8484\",   color.sec = \"#84EF84\" )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_sparkline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add sparkline to datagrid — add_sparkline","text":"grid grid column clumn transform","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_sparkline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add sparkline to datagrid — add_sparkline","text":"datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_sparkline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add sparkline to datagrid — add_sparkline","text":"","code":"grid <- mtcars |>   default_parsing() |>   overview_vars() |>   toastui::datagrid() |>   add_sparkline() grid      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theme based on unity — custom_theme","title":"Custom theme based on unity — custom_theme","text":"Custom theme based unity","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/custom_theme.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom theme based on unity — custom_theme","text":"","code":"custom_theme(   ...,   version = 5,   primary = \"#1E4A8F\",   secondary = \"#FF6F61\",   bootswatch = \"united\",   base_font = bslib::font_google(\"Montserrat\"),   heading_font = bslib::font_google(\"Public Sans\", wght = \"700\"),   code_font = bslib::font_google(\"Open Sans\") )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/custom_theme.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom theme based on unity — custom_theme","text":"... everything passed bslib::bs_theme()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/custom_theme.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom theme based on unity — custom_theme","text":"theme list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":null,"dir":"Reference","previous_headings":"","what":"Module to Convert Numeric to Factor — cut-variable","title":"Module to Convert Numeric to Factor — cut-variable","text":"module contain interface cut numeric several intervals.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module to Convert Numeric to Factor — cut-variable","text":"","code":"cut_variable_ui(id)  cut_variable_server(id, data_r = reactive(NULL))  modal_cut_variable(   id,   title = i18n(\"Convert Numeric to Factor\"),   easyClose = TRUE,   size = \"l\",   footer = NULL )  winbox_cut_variable(   id,   title = i18n(\"Convert Numeric to Factor\"),   options = shinyWidgets::wbOptions(),   controls = shinyWidgets::wbControls() )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module to Convert Numeric to Factor — cut-variable","text":"id Module ID. data_r shiny::reactive() function returning data.frame. title optional title dialog. easyClose TRUE, modal dialog can dismissed clicking outside dialog box, pressing Escape key. 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returning \"UTC\". #> [1] 01:00:20 02:10:20 01:00:20 02:10:20 <NA>     #> attr(,\"brks\") #> 01:00:20 #> 02:10:20 #> 03:02:21 #> Levels: 01:00:20 02:10:20 readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(2) #> [1] 1992-02-01 01:00:20 1992-02-01 01:00:20 1992-02-01 01:00:20 #> [4] 1992-02-01 01:00:20 1999-02-01 21:20:20 1992-02-01 01:00:20 #> Levels: 1992-02-01 01:00:20 1999-02-01 21:20:20 readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"weekday\") #> Error in cut.POSIXt(readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"weekday\"): invalid specification of 'breaks' readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"month_only\") #> Error in cut.POSIXt(readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"month_only\"): invalid specification of 'breaks' as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(2) #> [1] 1992-02-01 1992-02-01 1992-02-01 1992-02-01 1999-02-01 1992-02-01 #> Levels: 1992-02-01 1999-02-01 as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"weekday\") #> Error in cut.Date(as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"weekday\"): invalid specification of 'breaks'"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":null,"dir":"Reference","previous_headings":"","what":"Data correlations evaluation module — data-correlations","title":"Data correlations evaluation module — data-correlations","text":"Data correlations evaluation module Data correlations evaluation module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data correlations evaluation module — data-correlations","text":"","code":"data_correlations_ui(id, ...)  data_correlations_server(id, data, include.class = NULL, cutoff = 0.7, ...)  data_visuals_ui(id, tab_title = \"Plots\", ...)  data_visuals_server(id, data, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data correlations evaluation module — data-correlations","text":"id Module id. (Use 'ns(\"id\")') ... ignored data data color.main main color color.sec secondary color","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data correlations evaluation module — data-correlations","text":"Shiny ui module shiny server module Shiny ui module shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Title — data-plots","title":"Title — data-plots","text":"Title Wrapper create plot based provided type Nice horizontal stacked bars (Grotta bars) Beatiful violin plot Beautiful violin plot Beautiful sankey plot option split tertiary group","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title — data-plots","text":"","code":"plot_ridge(data, x, y, z = NULL, ...)  create_plot(data, type, x, y, z = NULL, ...)  plot_hbars(data, x, y, z = NULL)  plot_violin(data, x, y, z = NULL)  plot_scatter(data, x, y, z = NULL)  plot_sankey(data, x, y, z = NULL, color.group = \"x\", colors = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title — data-plots","text":"... ignored now type plot type (derived possible_plots() matches custom function)","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title — data-plots","text":"ggplot2 object ggplot2 object ggplot2 object ggplot2 object ggplot2 object ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Title — data-plots","text":"","code":"mtcars |>   default_parsing() |>   plot_ridge(x = \"mpg\", y = \"cyl\") #> Picking joint bandwidth of 1.38  mtcars |> plot_ridge(x = \"mpg\", y = \"cyl\", z = \"gear\") #> Picking joint bandwidth of 1.52 #> Warning: The following aesthetics were dropped during statistical transformation: y and #> fill. #> ℹ This can happen when ggplot fails to infer the correct grouping structure in #>   the data. #> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical #>   variable into a factor? #> Error in ggridges::geom_density_ridges(): Problem while setting up geom. #> ℹ Error occurred in the 1st layer. #> Caused by error in `compute_geom_1()`: #> ! `geom_density_ridges()` requires the following missing aesthetics: y. create_plot(mtcars, \"plot_violin\", \"mpg\", \"cyl\") #> Error in if (!z %in% names(data)) {    z <- NULL}: argument is of length zero mtcars |> plot_hbars(x = \"carb\", y = \"cyl\") #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale.  mtcars |> plot_hbars(x = \"carb\", y = NULL) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale.  mtcars |> plot_violin(x = \"mpg\", y = \"cyl\", z = \"gear\") #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 1: `cyl = 4`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 1: `cyl = 4`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 2: `cyl = 6`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 2: `cyl = 6`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.  mtcars |> plot_scatter(x = \"mpg\", y = \"wt\")  ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) ds |> plot_sankey(\"first\", \"last\") #> Loading required package: ggplot2  ds |> plot_sankey(\"first\", \"last\", color.group = \"y\")  ds |> plot_sankey(\"first\", \"last\", z = \"g\", color.group = \"y\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Data summary module — data-summary","title":"Data summary module — data-summary","text":"Data summary module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data summary module — data-summary","text":"","code":"data_summary_ui(id)  data_summary_server(id, data, color.main, color.sec, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data summary module — data-summary","text":"id Module id. (Use 'ns(\"id\")') data data color.main main color color.sec secondary color ... arguments passed toastui::datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data summary module — data-summary","text":"Shiny ui module shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Defaults qmd formats — default_format_arguments","title":"Defaults qmd formats — default_format_arguments","text":"Defaults qmd formats","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Defaults qmd formats — default_format_arguments","text":"","code":"default_format_arguments()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Defaults qmd formats — default_format_arguments","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":null,"dir":"Reference","previous_headings":"","what":"Default data parsing — default_parsing","title":"Default data parsing — default_parsing","text":"Default data parsing","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default data parsing — default_parsing","text":"","code":"default_parsing(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default data parsing — default_parsing","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default data parsing — default_parsing","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Default data parsing — default_parsing","text":"","code":"mtcars |> str() #> 'data.frame':\t32 obs. of  11 variables: #>  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num  160 160 108 258 360 ... #>  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num  16.5 17 18.6 19.4 17 ... #>  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num  1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num  4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num  4 4 1 1 2 1 4 2 2 4 ... mtcars |>   default_parsing() |>   str() #> tibble [32 × 11] (S3: tbl_df/tbl/data.frame) #>  $ mpg : num [1:32] 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : Factor w/ 3 levels \"4\",\"6\",\"8\": 2 2 1 2 3 2 3 1 1 2 ... #>  $ disp: num [1:32] 160 160 108 258 360 ... #>  $ hp  : num [1:32] 110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num [1:32] 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num [1:32] 2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num [1:32] 16.5 17 18.6 19.4 17 ... #>  $ vs  : Factor w/ 2 levels \"0\",\"1\": 1 1 2 2 1 2 1 2 2 2 ... #>  $ am  : Factor w/ 2 levels \"0\",\"1\": 2 2 2 1 1 1 1 1 1 1 ... #>  $ gear: Factor w/ 3 levels \"3\",\"4\",\"5\": 2 2 2 1 1 1 1 2 2 2 ... #>  $ carb: Factor w/ 6 levels \"1\",\"2\",\"3\",\"4\",..: 4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":null,"dir":"Reference","previous_headings":"","what":"Factorize variables in data.frame — factorize","title":"Factorize variables in data.frame — factorize","text":"Factorize variables data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Factorize variables in data.frame — factorize","text":"","code":"factorize(data, vars)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Factorize variables in data.frame — factorize","text":"data data.frame vars variables force factorize","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Factorize variables in data.frame — factorize","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":null,"dir":"Reference","previous_headings":"","what":"Title — file_export","title":"Title — file_export","text":"Title","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title — file_export","text":"","code":"file_export(data, output.format = c(\"df\", \"teal\", \"list\"), filename, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title — file_export","text":"data data output.format output filename filename ... passed ","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title — file_export","text":"data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":null,"dir":"Reference","previous_headings":"","what":"Merges list of named arguments for qmd header generation — format_writer","title":"Merges list of named arguments for qmd header generation — format_writer","text":"Merges list named arguments qmd header generation","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merges list of named arguments for qmd header generation — format_writer","text":"","code":"format_writer(data, name)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merges list of named arguments for qmd header generation — format_writer","text":"data vector name name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merges list of named arguments for qmd header generation — format_writer","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the function options based on the selected function description — get_fun_options","title":"Get the function options based on the selected function description — get_fun_options","text":"Get function options based selected function description","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the function options based on the selected function description — get_fun_options","text":"","code":"get_fun_options(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the function options based on the selected function description — get_fun_options","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the function options based on the selected function description — get_fun_options","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the function options based on the selected function description — get_fun_options","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(mpg) |>   possible_functions(design = \"cross-sectional\") |>   (\\(.x){     .x[[1]]   })() |>   get_fun_options() #> $lm #> $lm$descr #> [1] \"Linear regression model\" #>  #> $lm$design #> [1] \"cross-sectional\" #>  #> $lm$out.type #> [1] \"continuous\" #>  #> $lm$fun #> [1] \"stats::lm\" #>  #> $lm$args.list #> NULL #>  #> $lm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $lm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $lm$table.args.list #> $lm$table.args.list$exponentiate #> [1] FALSE #>  #>  #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Print label, and if missing print variable name — get_label","title":"Print label, and if missing print variable name — get_label","text":"Print label, missing print variable name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print label, and if missing print variable name — get_label","text":"","code":"get_label(data, var = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print label, and if missing print variable name — get_label","text":"data vector data 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get_plot_options","title":"Get the function options based on the selected function description — get_plot_options","text":"Get function options based selected function description","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the function options based on the selected function description — get_plot_options","text":"","code":"get_plot_options(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the function options based on the selected function description — get_plot_options","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the function options based on the selected function description — get_plot_options","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the function options based on the selected function description — get_plot_options","text":"","code":"ls <- mtcars |>   default_parsing() |>   dplyr::pull(mpg) |>   possible_plots() |>   (\\(.x){     .x[[1]]   })() |>   get_plot_options()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"function follows idea comment: https://stackoverflow.com/questions/38983179/-call--function--r-without-loading--package","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"","code":"getfun(x)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"x function function name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"function character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"","code":"getfun(\"stats::lm\") #> function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> } #> <bytecode: 0x564b9a27c918> #> <environment: namespace:stats>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":null,"dir":"Reference","previous_headings":"","what":"GGplot default theme for plotting export objects — gg_theme_export","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"GGplot default theme plotting export objects","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"","code":"gg_theme_export()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"data ggplot 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gg_theme_shiny","text":"","code":"gg_theme_shiny()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"data ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/index_embed.html","id":null,"dir":"Reference","previous_headings":"","what":"Split vector by an index and embed addition — index_embed","title":"Split vector by an index and embed addition — index_embed","text":"Split vector index embed 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class — is_any_class","text":"Test class","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test class — is_any_class","text":"","code":"is_any_class(data, class.vec)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test class — is_any_class","text":"data data class.vec vector class names test","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test class — is_any_class","text":"factor","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test class — is_any_class","text":"","code":"if (FALSE) { # \\dontrun{ vapply(REDCapCAST::redcapcast_data, \\(.x){   is_any_class(.x, c(\"hms\", \"Date\", \"POSIXct\", \"POSIXt\")) }, logical(1)) } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"Checks elements vector equally spaced indication ID","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"","code":"is_consecutive(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"logical","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"","code":"1:10 |> is_consecutive() #> [1] TRUE sample(1:100,40) |> is_consecutive() #> [1] FALSE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":null,"dir":"Reference","previous_headings":"","what":"Test is date/datetime/time — is_datetime","title":"Test is date/datetime/time — is_datetime","text":"Test date/datetime/time","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test is date/datetime/time — is_datetime","text":"","code":"is_datetime(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test is date/datetime/time — is_datetime","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test is date/datetime/time — is_datetime","text":"factor","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test is date/datetime/time — is_datetime","text":"","code":"vapply(REDCapCAST::redcapcast_data, is_datetime, logical(1)) #>                    record_id            redcap_event_name  #>                        FALSE                        FALSE  #>     redcap_repeat_instrument       redcap_repeat_instance  #>                        FALSE                        FALSE  #>                          cpr                    inclusion  #>                        FALSE                         TRUE  #>               inclusion_time                          dob  #>                         TRUE                         TRUE  #>                          age                  age_integer  #>                        FALSE                        FALSE  #>                          sex                 cohabitation  #>                        FALSE                        FALSE  #>                 hypertension                     diabetes  #>                        FALSE                        FALSE  #>                       region baseline_data_start_complete  #>                        FALSE                        FALSE  #>                 mrs_assessed                     mrs_date  #>                        FALSE                         TRUE  #>                    mrs_score                 mrs_complete  #>                        FALSE                        FALSE  #>                      con_mrs                     con_calc  #>                        FALSE                        FALSE  #>           consensus_complete               event_datetime  #>                        FALSE                         TRUE  #>                    event_age                   event_type  #>                        FALSE                        FALSE  #>           new_event_complete  #>                        FALSE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Title — is_valid_redcap_url","title":"Title — is_valid_redcap_url","text":"Title","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title — is_valid_redcap_url","text":"","code":"is_valid_redcap_url(url)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title — is_valid_redcap_url","text":"url","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Title — is_valid_redcap_url","text":"","code":"url <- c(   \"www.example.com\",   \"http://example.com\",   \"https://redcap.your.inst/api/\" ) is_valid_redcap_url(url) #> [1] FALSE FALSE  TRUE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate REDCap token — is_valid_token","title":"Validate REDCap token — is_valid_token","text":"Validate REDCap token","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate REDCap token — is_valid_token","text":"","code":"is_valid_token(token, pattern_env = NULL, nchar = 32)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate REDCap token — is_valid_token","text":"token token pattern_env pattern","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate REDCap token — is_valid_token","text":"","code":"token <- paste(sample(c(1:9, LETTERS[1:6]), 32, TRUE), collapse = \"\") is_valid_token(token) #> [1] TRUE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily launch the freesearcheR app — launch_freesearcheR","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"Easily launch freesearcheR app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"","code":"launch_freesearcheR(...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"... passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":null,"dir":"Reference","previous_headings":"","what":"Line breaking at given number of characters for nicely plotting labels — line_break","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"Line breaking given number characters nicely plotting labels","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"","code":"line_break(data, lineLength = 20)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"lineLength","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny UI module to load a data file — m_datafileUI","title":"Shiny UI module to load a data file — m_datafileUI","text":"Shiny UI module load data file","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny UI module to load a data file — m_datafileUI","text":"","code":"m_datafileUI(id)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny UI module to load a data file — m_datafileUI","text":"id id","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny UI module to load a data file — m_datafileUI","text":"shiny UI","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"Wrapper pivot gtsummary table data long plotting","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"","code":"merge_long(list, model.names)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"list custom regression models list model.names names models include","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to modify quarto file to render specific formats — modify_qmd","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"Wrapper modify quarto file render specific formats","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"","code":"modify_qmd(file, format)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"file filename format desired output","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"none","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Outcome data type assessment — outcome_type","title":"Outcome data type assessment — outcome_type","text":"Outcome data type assessment","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Outcome data type assessment — outcome_type","text":"","code":"outcome_type(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Outcome data type assessment — outcome_type","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Outcome data type assessment — outcome_type","text":"outcome type","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Outcome data type assessment — outcome_type","text":"","code":"mtcars |>   default_parsing() |>   lapply(outcome_type) #> $mpg #> [1] \"continuous\" #>  #> $cyl #> [1] \"ordinal\" #>  #> $disp #> [1] \"continuous\" #>  #> $hp #> [1] \"continuous\" #>  #> $drat #> [1] \"continuous\" #>  #> $wt #> [1] \"continuous\" #>  #> $qsec #> [1] \"continuous\" #>  #> $vs #> [1] \"dichotomous\" #>  #> $am #> [1] \"dichotomous\" #>  #> $gear #> [1] \"ordinal\" #>  #> $carb #> [1] \"ordinal\" #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a data overview data.frame ready for sparklines — overview_vars","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"Create data overview data.frame ready sparklines","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"","code":"overview_vars(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"","code":"mtcars |> overview_vars() #> # A tibble: 11 × 7 #>    class   type    name  n_missing p_complete n_unique vals         #>    <chr>   <chr>   <chr>     <dbl>      <dbl>    <int> <named list> #>  1 numeric numeric mpg           0          1       25 <dbl [32]>   #>  2 numeric numeric cyl           0          1        3 <dbl [32]>   #>  3 numeric numeric disp          0          1       27 <dbl [32]>   #>  4 numeric numeric hp            0          1       22 <dbl [32]>   #>  5 numeric numeric drat          0          1       22 <dbl [32]>   #>  6 numeric numeric wt            0          1       29 <dbl [32]>   #>  7 numeric numeric qsec          0          1       30 <dbl [32]>   #>  8 numeric numeric vs            0          1        2 <dbl [32]>   #>  9 numeric numeric am            0          1        2 <dbl [32]>   #> 10 numeric numeric gear          0          1        3 <dbl [32]>   #> 11 numeric numeric carb          0          1        6 <dbl [32]>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"Regression coef plot gtsummary. Slightly modified pass arguments","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"","code":"# S3 method for class 'tbl_regression' plot(x, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"x (tbl_regression, tbl_uvregression) 'tbl_regression' 'tbl_uvregression' object ... arguments passed ggstats::ggcoef_plot(...)","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"","code":"if (FALSE) { # \\dontrun{ mod <- lm(mpg ~ ., mtcars) p <- mod |>   gtsummary::tbl_regression() |>   plot(colour = \"variable\") } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":null,"dir":"Reference","previous_headings":"","what":"Beautiful sankey plot — plot_sankey_single","title":"Beautiful sankey plot — plot_sankey_single","text":"Beautiful sankey plot","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Beautiful sankey plot — plot_sankey_single","text":"","code":"plot_sankey_single(data, x, y, color.group = \"x\", colors = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Beautiful sankey plot — plot_sankey_single","text":"colors","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Beautiful sankey plot — plot_sankey_single","text":"ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Beautiful sankey plot — plot_sankey_single","text":"","code":"ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) ds |> plot_sankey_single(\"first\", \"last\")  ds |> plot_sankey_single(\"first\", \"last\", color.group = \"y\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Get possible regression models — possible_functions","title":"Get possible regression models — possible_functions","text":"Get possible regression models","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get possible regression models — possible_functions","text":"","code":"possible_functions(data, design = c(\"cross-sectional\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get possible regression models — possible_functions","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get possible regression models — possible_functions","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get possible regression models — possible_functions","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(\"cyl\") |>   possible_functions(design = \"cross-sectional\") #> [1] \"Ordinal logistic regression model\"  mtcars |>   default_parsing() |>   dplyr::select(\"cyl\") |>   possible_functions(design = \"cross-sectional\") #> [1] \"Ordinal logistic regression model\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Get possible regression models — possible_plots","title":"Get possible regression models — possible_plots","text":"Get possible regression models","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get possible regression models — possible_plots","text":"","code":"possible_plots(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get possible regression models — possible_plots","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get possible regression models — possible_plots","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get possible regression models — possible_plots","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(\"cyl\") |>   possible_plots() #> [1] \"Stacked horizontal bars\" \"Violin plot\"             #> [3] \"Sankey plot\"              mtcars |>   default_parsing() |>   dplyr::select(\"mpg\") |>   possible_plots() #> [1] \"Violin plot\"  \"Ridge plot\"   \"Scatter plot\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Flexible file import based on extension — read_input","title":"Flexible file import based on extension — read_input","text":"Flexible file import based extension","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(file, consider.na = c(\"NA\", \"\\\"\\\"\", \"\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flexible file import based on extension — read_input","text":"file file name consider.na character vector strings consider NAs","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Flexible file import based on extension — read_input","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(\"https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv\") #> Rows: 28 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> dbl (8): id, ab, age, imm, vis, ver, att, del #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> # A tibble: 28 × 8 #>       id    ab   age   imm   vis   ver   att   del #>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1     1     1    74    38    35    30    29    35 #>  2     1     2    69    36    36    21    27    37 #>  3     2     1    63    32    31    26    34    38 #>  4     2     2    64    37    34    26    36    46 #>  5     3     1    69    39    33    31    47    29 #>  6     3     2    70    40    36    31    46    25 #>  7     4     1    79    44    37    20    37    36 #>  8     4     2    81    35    36    31    37    40 #>  9     5     1    77    35    26    17    20    36 #> 10     5     2    80    29    34    18    23    36 #> # ℹ 18 more rows"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny module to browser and export REDCap data — m_redcap_readUI","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"Shiny module browser export REDCap data Test app redcap_read_shiny_module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"","code":"m_redcap_readUI(id, include_title = TRUE)  m_redcap_readServer(id)  redcap_demo_app()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"id Namespace id include_title logical include title","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"shiny ui element shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"","code":"if (FALSE) { # \\dontrun{ redcap_demo_app() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a regression model programatically — regression_model","title":"Create a regression model programatically — regression_model","text":"Output concatenated list model information model","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a regression model programatically — regression_model","text":"","code":"regression_model(   data,   outcome.str,   auto.mode = FALSE,   formula.str = NULL,   args.list = NULL,   fun = NULL,   vars = NULL,   ... )  regression_model_uv(   data,   outcome.str,   args.list = NULL,   fun = NULL,   vars = NULL,   ... )  regression_model_list(   data,   outcome.str,   fun.descr,   fun = NULL,   formula.str = NULL,   args.list = NULL,   vars = NULL,   ... )  regression_model_uv_list(   data,   outcome.str,   fun.descr,   fun = NULL,   formula.str = NULL,   args.list = NULL,   vars = NULL,   ... )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a regression model programatically — regression_model","text":"data data outcome.str name outcome variable auto.mode Make assumptions function dependent outcome data format. Overwrites arguments. formula.str custom formula glue string. Default NULL. args.list custom character string converted using argsstring2list() list arguments. Default NULL. fun name custom function. Default NULL. vars character vector variables include ... ignored fun.descr Description chosen function matching description \"supported_functions()\"","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a regression model programatically — regression_model","text":"object standard class fun object standard class fun list list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a regression model programatically — regression_model","text":"","code":"gtsummary::trial |>   regression_model(outcome.str = \"age\") #>  #> Call: #> (function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> })(formula = age ~ trt + marker + stage + grade + response +  #>     death + ttdeath, data = structure(list(trt = structure(c(1L,  #> 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L,  #> 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L,  #> 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #> 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L,  #> 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L,  #> 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L,  #> 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L,  #> 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,  #> 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\", \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(0L,  #>     1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L,  #>     0L, 0L, 1L, 0L, NA, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     0L, 0L, 0L, NA, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     1L, 1L, NA, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, NA, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 0L,  #>     0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, NA, 0L, 1L,  #>     0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L,  #>     1L, 1L, 0L, 0L), label = \"Tumor Response\"), death = structure(c(0L,  #>     0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L,  #>     0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L,  #>     1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L,  #>     1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L,  #>     1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L,  #>     0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 1L, 0L), label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)    trtDrug B       marker      stageT2      stageT3      stageT4   #>     45.9247      -0.4052      -0.1435       2.0519       2.4437      -3.1573   #>     gradeII     gradeIII     response        death      ttdeath   #>      0.1750       1.6855       4.9885       3.0775      -0.1394   #>  gtsummary::trial |>   regression_model(     outcome.str = \"age\",     auto.mode = FALSE,     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) #>  #> Call: #> (function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> })(formula = age ~ ., data = structure(list(trt = structure(c(1L,  #> 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L,  #> 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L,  #> 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #> 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L,  #> 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L,  #> 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L,  #> 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L,  #> 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,  #> 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\", \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(0L,  #>     1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L,  #>     0L, 0L, 1L, 0L, NA, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     0L, 0L, 0L, NA, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     1L, 1L, NA, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, NA, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 0L,  #>     0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, NA, 0L, 1L,  #>     0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L,  #>     1L, 1L, 0L, 0L), label = \"Tumor Response\"), death = structure(c(0L,  #>     0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L,  #>     0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L,  #>     1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L,  #>     1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L,  #>     1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L,  #>     0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 1L, 0L), label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)    trtDrug B       marker      stageT2      stageT3      stageT4   #>     45.9247      -0.4052      -0.1435       2.0519       2.4437      -3.1573   #>     gradeII     gradeIII     response        death      ttdeath   #>      0.1750       1.6855       4.9885       3.0775      -0.1394   #>  gtsummary::trial |>   default_parsing() |>   regression_model(     outcome.str = \"trt\",     auto.mode = FALSE,     fun = \"stats::glm\",     args.list = list(family = binomial(link = \"logit\"))   ) #>  #> Call:  (function (formula, family = gaussian, data, weights, subset,  #>     na.action, start = NULL, etastart, mustart, offset, control = list(...),  #>     model = TRUE, method = \"glm.fit\", x = FALSE, y = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, ...)  #> { #>     cal <- match.call() #>     if (is.character(family))  #>         family <- get(family, mode = \"function\", envir = parent.frame()) #>     if (is.function(family))  #>         family <- family() #>     if (is.null(family$family)) { #>         print(family) #>         stop(\"'family' not recognized\") #>     } #>     if (missing(data))  #>         data <- environment(formula) #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"etastart\", \"mustart\", \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (identical(method, \"model.frame\"))  #>         return(mf) #>     if (!is.character(method) && !is.function(method))  #>         stop(\"invalid 'method' argument\") #>     if (identical(method, \"glm.fit\"))  #>         control <- do.call(\"glm.control\", control) #>     mt <- attr(mf, \"terms\") #>     Y <- model.response(mf, \"any\") #>     if (length(dim(Y)) == 1L) { #>         nm <- rownames(Y) #>         dim(Y) <- NULL #>         if (!is.null(nm))  #>             names(Y) <- nm #>     } #>     X <- if (!is.empty.model(mt))  #>         model.matrix(mt, mf, contrasts) #>     else matrix(, NROW(Y), 0L) #>     weights <- as.vector(model.weights(mf)) #>     if (!is.null(weights) && !is.numeric(weights))  #>         stop(\"'weights' must be a numeric vector\") #>     if (!is.null(weights) && any(weights < 0))  #>         stop(\"negative weights not allowed\") #>     offset <- as.vector(model.offset(mf)) #>     if (!is.null(offset)) { #>         if (length(offset) != NROW(Y))  #>             stop(gettextf(\"number of offsets is %d should equal %d (number of observations)\",  #>                 length(offset), NROW(Y)), domain = NA) #>     } #>     mustart <- model.extract(mf, \"mustart\") #>     etastart <- model.extract(mf, \"etastart\") #>     fit <- eval(call(if (is.function(method)) \"method\" else method,  #>         x = X, y = Y, weights = weights, start = start, etastart = etastart,  #>         mustart = mustart, offset = offset, family = family,  #>         control = control, intercept = attr(mt, \"intercept\") >  #>             0L, singular.ok = singular.ok)) #>     if (length(offset) && attr(mt, \"intercept\") > 0L) { #>         fit2 <- eval(call(if (is.function(method)) \"method\" else method,  #>             x = X[, \"(Intercept)\", drop = FALSE], y = Y, mustart = fit$fitted.values,  #>             weights = weights, offset = offset, family = family,  #>             control = control, intercept = TRUE)) #>         if (!fit2$converged)  #>             warning(\"fitting to calculate the null deviance did not converge -- increase 'maxit'?\") #>         fit$null.deviance <- fit2$deviance #>     } #>     if (model)  #>         fit$model <- mf #>     fit$na.action <- attr(mf, \"na.action\") #>     if (x)  #>         fit$x <- X #>     if (!y)  #>         fit$y <- NULL #>     structure(c(fit, list(call = cal, formula = formula, terms = mt,  #>         data = data, offset = offset, control = control, method = method,  #>         contrasts = attr(X, \"contrasts\"), xlevels = .getXlevels(mt,  #>             mf))), class = c(fit$class, c(\"glm\", \"lm\"))) #> })(formula = trt ~ age + marker + stage + grade + response +  #>     death + ttdeath, family = structure(list(family = \"binomial\",  #>     link = \"logit\", linkfun = function (mu)  #>     .Call(C_logit_link, mu), linkinv = function (eta)  #>     .Call(C_logit_linkinv, eta), variance = function (mu)  #>     mu * (1 - mu), dev.resids = function (y, mu, wt)  #>     .Call(C_binomial_dev_resids, y, mu, wt), aic = function (y,  #>         n, mu, wt, dev)  #>     { #>         m <- if (any(n > 1))  #>             n #>         else wt #>         -2 * sum(ifelse(m > 0, (wt/m), 0) * dbinom(round(m *  #>             y), round(m), mu, log = TRUE)) #>     }, mu.eta = function (eta)  #>     .Call(C_logit_mu_eta, eta), initialize = { #>         if (NCOL(y) == 1) { #>             if (is.factor(y))  #>                 y <- y != levels(y)[1L] #>             n <- rep.int(1, nobs) #>             y[weights == 0] <- 0 #>             if (any(y < 0 | y > 1))  #>                 stop(\"y values must be 0 <= y <= 1\") #>             mustart <- (weights * y + 0.5)/(weights + 1) #>             m <- weights * y #>             if (\"binomial\" == \"binomial\" && any(abs(m - round(m)) >  #>                 0.001))  #>                 warning(gettextf(\"non-integer #successes in a %s glm!\",  #>                   \"binomial\"), domain = NA) #>         } #>         else if (NCOL(y) == 2) { #>             if (\"binomial\" == \"binomial\" && any(abs(y - round(y)) >  #>                 0.001))  #>                 warning(gettextf(\"non-integer counts in a %s glm!\",  #>                   \"binomial\"), domain = NA) #>             n <- (y1 <- y[, 1L]) + y[, 2L] #>             y <- y1/n #>             if (any(n0 <- n == 0))  #>                 y[n0] <- 0 #>             weights <- weights * n #>             mustart <- (n * y + 0.5)/(n + 1) #>         } #>         else stop(gettextf(\"for the '%s' family, y must be a vector of 0 and 1's\\nor a 2 column matrix where col 1 is no. successes and col 2 is no. failures\",  #>             \"binomial\"), domain = NA) #>     }, validmu = function (mu)  #>     all(is.finite(mu)) && all(mu > 0 & mu < 1), valideta = function (eta)  #>     TRUE, simulate = function (object, nsim)  #>     { #>         ftd <- fitted(object) #>         n <- length(ftd) #>         ntot <- n * nsim #>         wts <- object$prior.weights #>         if (any(wts%%1 != 0))  #>             stop(\"cannot simulate from non-integer prior.weights\") #>         if (!is.null(m <- object$model)) { #>             y <- model.response(m) #>             if (is.factor(y)) { #>                 yy <- factor(1 + rbinom(ntot, size = 1, prob = ftd),  #>                   labels = levels(y)) #>                 split(yy, rep(seq_len(nsim), each = n)) #>             } #>             else if (is.matrix(y) && ncol(y) == 2) { #>                 yy <- vector(\"list\", nsim) #>                 for (i in seq_len(nsim)) { #>                   Y <- rbinom(n, size = wts, prob = ftd) #>                   YY <- cbind(Y, wts - Y) #>                   colnames(YY) <- colnames(y) #>                   yy[[i]] <- YY #>                 } #>                 yy #>             } #>             else rbinom(ntot, size = wts, prob = ftd)/wts #>         } #>         else rbinom(ntot, size = wts, prob = ftd)/wts #>     }, dispersion = 1), class = \"family\"), data = structure(list( #>     trt = structure(c(1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,  #>     2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,  #>     2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L,  #>     2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #>     1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L,  #>     2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\",  #>     \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(1L,  #>     2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L,  #>     2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L,  #>     1L, 1L, 2L, 1L, NA, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L,  #>     2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L,  #>     1L, 1L, 1L, NA, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L,  #>     1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L, 1L, 2L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L,  #>     2L, 2L, NA, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, NA, 2L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L,  #>     1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, NA, 1L, 2L,  #>     1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L,  #>     2L, 2L, 1L, 1L), levels = c(\"0\", \"1\"), class = \"factor\", label = \"Tumor Response\"),  #>     death = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L,  #>     1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,  #>     2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L,  #>     2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L,  #>     1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,  #>     2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L,  #>     1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #>     1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,  #>     1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L,  #>     1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L,  #>     1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L), levels = c(\"0\",  #>     \"1\"), class = \"factor\", label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)          age       marker      stageT2      stageT3      stageT4   #>    1.652845    -0.002014    -0.259849     0.404341     0.117402    -0.002102   #>     gradeII     gradeIII    response1       death1      ttdeath   #>   -0.037012     0.022890     0.498952    -0.003916    -0.076073   #>  #> Degrees of Freedom: 172 Total (i.e. Null);  162 Residual #>   (27 observations deleted due to missingness) #> Null Deviance:\t    239.5  #> Residual Deviance: 230.9 \tAIC: 252.9 m <- mtcars |>   default_parsing() |>   regression_model(     outcome.str = \"mpg\",     auto.mode = FALSE,     fun = \"stats::lm\",     formula.str = \"{outcome.str}~{paste(vars,collapse='+')}\",     args.list = NULL,     vars = c(\"mpg\", \"cyl\")   )   broom::tidy(m) #> # A tibble: 3 × 5 #>   term        estimate std.error statistic  p.value #>   <chr>          <dbl>     <dbl>     <dbl>    <dbl> #> 1 (Intercept)    26.7      0.972     27.4  2.69e-22 #> 2 cyl6           -6.92     1.56      -4.44 1.19e- 4 #> 3 cyl8          -11.6      1.30      -8.90 8.57e-10 if (FALSE) { # \\dontrun{ gtsummary::trial |>   regression_model_uv(outcome.str = \"age\") gtsummary::trial |>   regression_model_uv(     outcome.str = \"age\",     fun = \"stats::lm\",     args.list = NULL   ) m <- gtsummary::trial |> regression_model_uv(   outcome.str = \"trt\",   fun = \"stats::glm\",   args.list = list(family = stats::binomial(link = \"logit\")) ) lapply(m,broom::tidy) |> dplyr::bind_rows() } # } if (FALSE) { # \\dontrun{ gtsummary::trial |>   regression_model(     outcome.str = \"age\",     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) ls <- regression_model_list(data = default_parsing(mtcars), outcome.str = \"cyl\", fun.descr = \"Ordinal logistic regression model\") summary(ls$model)  ls <- regression_model_list(data = default_parsing(gtsummary::trial), outcome.str = \"trt\", fun.descr = \"Logistic regression model\") tbl <- gtsummary::tbl_regression(ls$model, exponentiate = TRUE) m <- gtsummary::trial |>   default_parsing() |>   regression_model(     outcome.str = \"trt\",     fun = \"stats::glm\",     formula.str = \"{outcome.str}~.\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) tbl2 <- gtsummary::tbl_regression(m, exponentiate = TRUE) broom::tidy(ls$model) broom::tidy(m) } # } if (FALSE) { # \\dontrun{ gtsummary::trial |> regression_model_uv(   outcome.str = \"trt\",   fun = \"stats::glm\",   args.list = list(family = stats::binomial(link = \"logit\")) ) |> lapply(broom::tidy) |> dplyr::bind_rows() ms <- regression_model_uv_list(data = default_parsing(mtcars), outcome.str = \"mpg\", fun.descr = \"Linear regression model\") lapply(ms$model,broom::tidy) |> dplyr::bind_rows() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Create table of regression model — regression_table","title":"Create table of regression model — regression_table","text":"Create table regression model","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create table of regression model — regression_table","text":"","code":"regression_table(x, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create table of regression model — regression_table","text":"x regression model ... passed methods args.list list arguments passed 'fun'. fun function use table creation. Default \"gtsummary::tbl_regression\".","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create table of regression model — regression_table","text":"object standard class fun","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create table of regression model — regression_table","text":"","code":"if (FALSE) { # \\dontrun{ tbl <- gtsummary::trial |>   regression_model(     outcome.str = \"stage\",     fun = \"MASS::polr\"   ) |>   regression_table(args.list = list(\"exponentiate\" = TRUE)) gtsummary::trial |>   regression_model(     outcome.str = \"age\",     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) |>   regression_table() |> plot() gtsummary::trial |>   regression_model(     outcome.str = \"trt\",     fun = \"stats::glm\",     args.list = list(family = binomial(link = \"logit\"))   ) |>   regression_table() gtsummary::trial |>   regression_model_uv(     outcome.str = \"trt\",     fun = \"stats::glm\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) |>   regression_table() gtsummary::trial |>   regression_model_uv(     outcome.str = \"stage\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) |>   regression_table()  list(   \"Univariable\" = regression_model_uv,   \"Multivariable\" = regression_model ) |>   lapply(\\(.fun){     do.call(       .fun,       c(         list(data = gtsummary::trial),         list(outcome.str = \"stage\")       )     )   }) |>   purrr::map(regression_table) |>   tbl_merge()   } # } regression_table <- function(x, ...) {   UseMethod(\"regression_table\") }  #' @rdname regression_table #' @export regression_table.list <- function(x, ...) {   x |>     purrr::map(\\(.m){       regression_table(x = .m, ...) |>         gtsummary::add_n()     }) |>     gtsummary::tbl_stack() }  #' @rdname regression_table #' @export regression_table.default <- function(x, ..., args.list = NULL, fun = \"gtsummary::tbl_regression\") {   # Stripping custom class   class(x) <- class(x)[class(x) != \"freesearcher_model\"]    if (any(c(length(class(x)) != 1, class(x) != \"lm\"))) {     if (!\"exponentiate\" %in% names(args.list)) {       args.list <- c(args.list, list(exponentiate = TRUE))     }   }    out <- do.call(getfun(fun), c(list(x = x), args.list))   out |>     gtsummary::add_glance_source_note() # |>   # gtsummary::bold_p() }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Removes columns with completenes below cutoff — remove_empty_cols","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"Removes columns completenes cutoff","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"","code":"remove_empty_cols(data, cutoff = 0.7)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"data data frame cutoff numeric","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"data frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"","code":"data.frame(a=1:10,b=NA, c=c(2,NA)) |> remove_empty_cols(cutoff=.5) #>     a  c #> 1   1  2 #> 2   2 NA #> 3   3  2 #> 4   4 NA #> 5   5  2 #> 6   6 NA #> 7   7  2 #> 8   8 NA #> 9   9  2 #> 10 10 NA"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove NA labels — remove_na_attr","title":"Remove NA labels — remove_na_attr","text":"Remove NA labels","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove NA labels — remove_na_attr","text":"","code":"remove_na_attr(data, attr = \"label\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove NA labels — remove_na_attr","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove NA labels — remove_na_attr","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove NA labels — remove_na_attr","text":"","code":"ds <- mtcars |> lapply(\\(.x) REDCapCAST::set_attr(.x,label=NA,attr = \"label\")) ds |> remove_na_attr() |> str() #> tibble [32 × 11] (S3: tbl_df/tbl/data.frame) #>  $ mpg : num [1:32] 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num [1:32] 6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num [1:32] 160 160 108 258 360 ... #>  $ hp  : num [1:32] 110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num [1:32] 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num [1:32] 2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num [1:32] 16.5 17 18.6 19.4 17 ... #>  $ vs  : num [1:32] 0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num [1:32] 1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num [1:32] 4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num [1:32] 4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/freesearcheR/reference/sankey_ready.html","id":null,"dir":"Reference","previous_headings":"","what":"Readying data for sankey plot — sankey_ready","title":"Readying data for sankey plot — sankey_ready","text":"Readying data sankey plot","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/sankey_ready.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Readying data for sankey plot — sankey_ready","text":"","code":"sankey_ready(data, x, y, z = NULL, numbers = \"count\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/sankey_ready.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Readying data for sankey plot — sankey_ready","text":"z","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/sankey_ready.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Readying data for sankey plot — sankey_ready","text":"","code":"ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = sample(c(letters[1:4], NA), 100, TRUE, prob = c(rep(.23, 4), .08))) ds |> sankey_ready(\"first\", \"last\") #> # A tibble: 20 × 7 #>    first last      n gx.sum gy.sum lx          ly          #>    <fct> <chr> <int>  <int>  <int> <fct>       <fct>       #>  1 d     a         5     22     17 \"d\\n(n=22)\" \"a\\n(n=17)\" #>  2 d     b         8     22     25 \"d\\n(n=22)\" \"b\\n(n=25)\" #>  3 d     c         4     22     29 \"d\\n(n=22)\" \"c\\n(n=29)\" #>  4 d     d         4     22     22 \"d\\n(n=22)\" \"d\\n(n=22)\" #>  5 d     NA        1     22      7 \"d\\n(n=22)\" \"NA\\n(n=7)\" #>  6 b     a         1     32     17 \"b\\n(n=32)\" \"a\\n(n=17)\" #>  7 b     b        11     32     25 \"b\\n(n=32)\" \"b\\n(n=25)\" #>  8 b     c        12     32     29 \"b\\n(n=32)\" \"c\\n(n=29)\" #>  9 b     d         7     32     22 \"b\\n(n=32)\" \"d\\n(n=22)\" #> 10 b     NA        1     32      7 \"b\\n(n=32)\" \"NA\\n(n=7)\" #> 11 a     a         8     23     17 \"a\\n(n=23)\" \"a\\n(n=17)\" #> 12 a     b         2     23     25 \"a\\n(n=23)\" \"b\\n(n=25)\" #> 13 a     c         7     23     29 \"a\\n(n=23)\" \"c\\n(n=29)\" #> 14 a     d         4     23     22 \"a\\n(n=23)\" \"d\\n(n=22)\" #> 15 a     NA        2     23      7 \"a\\n(n=23)\" \"NA\\n(n=7)\" #> 16 c     a         3     23     17 \"c\\n(n=23)\" \"a\\n(n=17)\" #> 17 c     b         4     23     25 \"c\\n(n=23)\" \"b\\n(n=25)\" #> 18 c     c         6     23     29 \"c\\n(n=23)\" \"c\\n(n=29)\" #> 19 c     d         7     23     22 \"c\\n(n=23)\" \"d\\n(n=22)\" #> 20 c     NA        3     23      7 \"c\\n(n=23)\" \"NA\\n(n=7)\" ds |> sankey_ready(\"first\", \"last\", numbers = \"percentage\") #> # A tibble: 20 × 7 #>    first last      n gx.sum gy.sum lx         ly         #>    <fct> <chr> <int>  <int>  <int> <fct>      <fct>      #>  1 d     a         5     22     17 \"d\\n(22%)\" \"a\\n(17%)\" #>  2 d     b         8     22     25 \"d\\n(22%)\" \"b\\n(25%)\" #>  3 d     c         4     22     29 \"d\\n(22%)\" \"c\\n(29%)\" #>  4 d     d         4     22     22 \"d\\n(22%)\" \"d\\n(22%)\" #>  5 d     NA        1     22      7 \"d\\n(22%)\" \"NA\\n(7%)\" #>  6 b     a         1     32     17 \"b\\n(32%)\" \"a\\n(17%)\" #>  7 b     b        11     32     25 \"b\\n(32%)\" \"b\\n(25%)\" #>  8 b     c        12     32     29 \"b\\n(32%)\" \"c\\n(29%)\" #>  9 b     d         7     32     22 \"b\\n(32%)\" \"d\\n(22%)\" #> 10 b     NA        1     32      7 \"b\\n(32%)\" \"NA\\n(7%)\" #> 11 a     a         8     23     17 \"a\\n(23%)\" \"a\\n(17%)\" #> 12 a     b         2     23     25 \"a\\n(23%)\" \"b\\n(25%)\" #> 13 a     c         7     23     29 \"a\\n(23%)\" \"c\\n(29%)\" #> 14 a     d         4     23     22 \"a\\n(23%)\" \"d\\n(22%)\" #> 15 a     NA        2     23      7 \"a\\n(23%)\" \"NA\\n(7%)\" #> 16 c     a         3     23     17 \"c\\n(23%)\" \"a\\n(17%)\" #> 17 c     b         4     23     25 \"c\\n(23%)\" \"b\\n(25%)\" #> 18 c     c         6     23     29 \"c\\n(23%)\" \"c\\n(29%)\" #> 19 c     d         7     23     22 \"c\\n(23%)\" \"d\\n(22%)\" #> 20 c     NA        3     23      7 \"c\\n(23%)\" \"NA\\n(7%)\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the freesearcheR tool locally — shiny_freesearcheR","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"data.frames global environment accessible app.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"","code":"shiny_freesearcheR(...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"... arguments passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"","code":"if (FALSE) { # \\dontrun{ data(mtcars) shiny_freesearcheR(launch.browser = TRUE) } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"Specify format arguments include qmd header/frontmatter","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"","code":"specify_qmd_format(data, fileformat = c(\"docx\", \"odt\", \"pdf\", \"all\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"data vector fileformat format include","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily subset by data type function — subset_types","title":"Easily subset by data type function — subset_types","text":"Easily subset data type function","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily subset by data type function — subset_types","text":"","code":"subset_types(data, types, type.fun = outcome_type)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easily subset by data type function — subset_types","text":"data data types desired types type.fun function get type. Default outcome_type","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily subset by data type function — subset_types","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Easily subset by data type function — subset_types","text":"","code":"default_parsing(mtcars) |> subset_types(\"ordinal\") #> # A tibble: 32 × 3 #>    cyl   gear  carb  #>    <fct> <fct> <fct> #>  1 6     4     4     #>  2 6     4     4     #>  3 4     4     1     #>  4 6     3     1     #>  5 8     3     2     #>  6 6     3     1     #>  7 8     3     4     #>  8 4     4     2     #>  9 4     4     2     #> 10 6     4     4     #> # ℹ 22 more rows default_parsing(mtcars) |> subset_types(c(\"dichotomous\", \"ordinal\")) #> # A tibble: 32 × 5 #>    cyl   vs    am    gear  carb  #>    <fct> <fct> <fct> <fct> <fct> #>  1 6     0     1     4     4     #>  2 6     0     1     4     4     #>  3 4     1     1     4     1     #>  4 6     1     0     3     1     #>  5 8     0     0     3     2     #>  6 6     1     0     3     1     #>  7 8     0     0     3     4     #>  8 4     1     0     4     2     #>  9 4     1     0     4     2     #> 10 6     1     0     4     4     #> # ℹ 22 more rows #' default_parsing(mtcars) |> subset_types(\"factor\",class)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Implemented functions — supported_functions","title":"Implemented functions — supported_functions","text":"Library supported functions. list name \"descr\" element unique element list.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Implemented functions — supported_functions","text":"","code":"supported_functions()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Implemented functions — supported_functions","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Implemented functions — supported_functions","text":"","code":"supported_functions() #> $lm #> $lm$descr #> [1] \"Linear regression model\" #>  #> $lm$design #> [1] \"cross-sectional\" #>  #> $lm$out.type #> [1] \"continuous\" #>  #> $lm$fun #> [1] \"stats::lm\" #>  #> $lm$args.list #> NULL #>  #> $lm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $lm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $lm$table.args.list #> $lm$table.args.list$exponentiate #> [1] FALSE #>  #>  #>  #> $glm #> $glm$descr #> [1] \"Logistic regression model\" #>  #> $glm$design #> [1] \"cross-sectional\" #>  #> $glm$out.type #> [1] \"dichotomous\" #>  #> $glm$fun #> [1] \"stats::glm\" #>  #> $glm$args.list #> $glm$args.list$family #>  #> Family: binomial  #> Link function: logit  #>  #>  #>  #> $glm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $glm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $glm$table.args.list #> list() #>  #>  #> $polr #> $polr$descr #> [1] \"Ordinal logistic regression model\" #>  #> $polr$design #> [1] \"cross-sectional\" #>  #> $polr$out.type #> [1] \"ordinal\" #>  #> $polr$fun #> [1] \"MASS::polr\" #>  #> $polr$args.list #> $polr$args.list$Hess #> [1] TRUE #>  #> $polr$args.list$method #> [1] \"logistic\" #>  #>  #> $polr$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $polr$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $polr$table.args.list #> list() #>  #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Implemented functions — supported_plots","title":"Implemented functions — supported_plots","text":"Library supported functions. list name \"descr\" element unique element list. descr: Plot description primary.type: Primary variable data type (continuous, dichotomous ordinal) secondary.type: Secondary variable data type (continuous, dichotomous ordinal) secondary.extra: \"none\" NULL option choose none. tertiary.type: Tertiary variable data type (continuous, dichotomous ordinal)","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Implemented functions — supported_plots","text":"","code":"supported_plots()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Implemented functions — supported_plots","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Implemented functions — supported_plots","text":"","code":"supported_plots() |> str() #> List of 5 #>  $ plot_hbars  :List of 6 #>   ..$ descr          : chr \"Stacked horizontal bars\" #>   ..$ note           : chr \"A classical way of visualising the distribution of an ordinal scale like the modified Ranking Scale and known as Grotta bars\" #>   ..$ primary.type   : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: chr \"none\" #>  $ plot_violin :List of 6 #>   ..$ descr          : chr \"Violin plot\" #>   ..$ note           : chr \"A modern alternative to the classic boxplot to visualise data distribution\" #>   ..$ primary.type   : chr [1:3] \"continuous\" \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: chr \"none\" #>  $ plot_ridge  :List of 6 #>   ..$ descr          : chr \"Ridge plot\" #>   ..$ note           : chr \"An alternative option to visualise data distribution\" #>   ..$ primary.type   : chr \"continuous\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: NULL #>  $ plot_sankey :List of 6 #>   ..$ descr          : chr \"Sankey plot\" #>   ..$ note           : chr \"A way of visualising change between groups\" #>   ..$ primary.type   : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: NULL #>  $ plot_scatter:List of 6 #>   ..$ descr          : chr \"Scatter plot\" #>   ..$ note           : chr \"A classic way of showing the association between to variables\" #>   ..$ primary.type   : chr \"continuous\" #>   ..$ secondary.type : chr [1:2] \"continuous\" \"ordinal\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: NULL"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":null,"dir":"Reference","previous_headings":"","what":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"substitue gtsummary::tbl_merge, use list names tab spanner 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General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. Developers use General Public Licenses protect rights two steps: (1) assert copyright software, (2) offer License gives legal permission copy, distribute /modify software. secondary benefit defending users’ freedom improvements made alternate versions program, receive widespread use, become available developers incorporate. Many developers free software heartened encouraged resulting cooperation. However, case software used network servers, result may fail come . GNU General Public License permits making modified version letting public access server without ever releasing source code public. 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License explicitly affirms unlimited permission run unmodified Program. output running covered work covered License output, given content, constitutes covered work. License acknowledges rights fair use equivalent, provided copyright law. may make, run propagate covered works convey, without conditions long license otherwise remains force. may convey covered works others sole purpose make modifications exclusively , provide facilities running works, provided comply terms License conveying material control copyright. thus making running covered works must exclusively behalf, direction control, terms prohibit making copies copyrighted material outside relationship . Conveying circumstances permitted solely conditions stated . Sublicensing allowed; section 10 makes unnecessary.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_3-protecting-users-legal-rights-from-anti-circumvention-law","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"3. 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Access network may denied modification materially adversely affects operation network violates rules protocols communication across network. Corresponding Source conveyed, Installation Information provided, accord section must format publicly documented (implementation available public source code form), must require special password key unpacking, reading copying.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_7-additional-terms","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"7. Additional Terms.","title":"GNU Affero General Public License","text":"“Additional permissions” terms supplement terms License making exceptions one conditions. Additional permissions applicable entire Program shall treated though included License, extent valid applicable law. additional permissions apply part Program, part may used separately permissions, entire Program remains governed License without regard additional permissions. convey copy covered work, may option remove additional permissions copy, part . (Additional permissions may written require removal certain cases modify work.) may place additional permissions material, added covered work, can give appropriate copyright permission. 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Termination.","title":"GNU Affero General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. Termination rights section terminate licenses parties received copies rights License. rights terminated permanently reinstated, qualify receive new licenses material section 10.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_9-acceptance-not-required-for-having-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"9. Acceptance Not Required for Having Copies.","title":"GNU Affero General Public License","text":"required accept License order receive run copy Program. Ancillary propagation covered work occurring solely consequence using peer--peer transmission receive copy likewise require acceptance. However, nothing License grants permission propagate modify covered work. actions infringe copyright accept License. Therefore, modifying propagating covered work, indicate acceptance License .","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_10-automatic-licensing-of-downstream-recipients","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"10. Automatic Licensing of Downstream Recipients.","title":"GNU Affero General Public License","text":"time convey covered work, recipient automatically receives license original licensors, run, modify propagate work, subject License. responsible enforcing compliance third parties License. “entity transaction” transaction transferring control organization, substantially assets one, subdividing organization, merging organizations. propagation covered work results entity transaction, party transaction receives copy work also receives whatever licenses work party’s predecessor interest give previous paragraph, plus right possession Corresponding Source work predecessor interest, predecessor can get reasonable efforts. may impose restrictions exercise rights granted affirmed License. example, may impose license fee, royalty, charge exercise rights granted License, may initiate litigation (including cross-claim counterclaim lawsuit) alleging patent claim infringed making, using, selling, offering sale, importing Program portion .","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_11-patents","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"11. Patents.","title":"GNU Affero General Public License","text":"“contributor” copyright holder authorizes use License Program work Program based. work thus licensed called contributor’s “contributor version”. contributor’s “essential patent claims” patent claims owned controlled contributor, whether already acquired hereafter acquired, infringed manner, permitted License, making, using, selling contributor version, include claims infringed consequence modification contributor version. purposes definition, “control” includes right grant patent sublicenses manner consistent requirements License. contributor grants non-exclusive, worldwide, royalty-free patent license contributor’s essential patent claims, make, use, sell, offer sale, import otherwise run, modify propagate contents contributor version. following three paragraphs, “patent license” express agreement commitment, however denominated, enforce patent (express permission practice patent covenant sue patent infringement). “grant” patent license party means make agreement commitment enforce patent party. convey covered work, knowingly relying patent license, Corresponding Source work available anyone copy, free charge terms License, publicly available network server readily accessible means, must either (1) cause Corresponding Source available, (2) arrange deprive benefit patent license particular work, (3) arrange, manner consistent requirements License, extend patent license downstream recipients. “Knowingly relying” means actual knowledge , patent license, conveying covered work country, recipient’s use covered work country, infringe one identifiable patents country reason believe valid. , pursuant connection single transaction arrangement, convey, propagate procuring conveyance , covered work, grant patent license parties receiving covered work authorizing use, propagate, modify convey specific copy covered work, patent license grant automatically extended recipients covered work works based . patent license “discriminatory” include within scope coverage, prohibits exercise , conditioned non-exercise one rights specifically granted License. may convey covered work party arrangement third party business distributing software, make payment third party based extent activity conveying work, third party grants, parties receive covered work , discriminatory patent license () connection copies covered work conveyed (copies made copies), (b) primarily connection specific products compilations contain covered work, unless entered arrangement, patent license granted, prior 28 March 2007. Nothing License shall construed excluding limiting implied license defenses infringement may otherwise available applicable patent law.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_12-no-surrender-of-others-freedom","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"12. No Surrender of Others’ Freedom.","title":"GNU Affero General Public License","text":"conditions imposed (whether court order, agreement otherwise) contradict conditions License, excuse conditions License. convey covered work satisfy simultaneously obligations License pertinent obligations, consequence may convey . example, agree terms obligate collect royalty conveying convey Program, way satisfy terms License refrain entirely conveying Program.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_13-remote-network-interaction-use-with-the-gnu-general-public-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"13. Remote Network Interaction; Use with the GNU General Public License.","title":"GNU Affero General Public License","text":"Notwithstanding provision License, modify Program, modified version must prominently offer users interacting remotely computer network (version supports interaction) opportunity receive Corresponding Source version providing access Corresponding Source network server charge, standard customary means facilitating copying software. Corresponding Source shall include Corresponding Source work covered version 3 GNU General Public License incorporated pursuant following paragraph. Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU General Public License single combined work, convey resulting work. terms License continue apply part covered work, work combined remain governed version 3 GNU General Public License.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License.","title":"GNU Affero General Public License","text":"Free Software Foundation may publish revised /new versions GNU Affero General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU Affero General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU Affero General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU Affero General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty.","title":"GNU Affero General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability.","title":"GNU Affero General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16.","title":"GNU Affero General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU Affero General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. software can interact users remotely computer network, also make sure provides way users get source. example, program web application, interface display “Source” link leads users archive code. many ways offer source, different solutions better different programs; see section 13 specific requirements. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU AGPL, see https://www.gnu.org/licenses/.","code":"<one line to give the program's name and a brief idea of what it does.>     Copyright (C) <year>  <name of author>      This program is free software: you can redistribute it and/or modify     it under the terms of the GNU Affero General Public License as     published by the Free Software Foundation, either version 3 of the     License, or (at your option) any later version.      This program is distributed in the hope that it will be useful,     but WITHOUT ANY WARRANTY; without even the implied warranty of     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the     GNU Affero General Public License for more details.      You should have received a copy of the GNU Affero General Public License     along with this program.  If not, see <https://www.gnu.org/licenses/>."},{"path":"https://agdamsbo.github.io/freesearcheR/QA.html","id":null,"dir":"","previous_headings":"","what":"Questions and answers","title":"Questions and answers","text":"complete instructions set available, collection questions answers project use app.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/QA.html","id":"are-you-keeping-the-uploaded-data","dir":"","previous_headings":"","what":"Are you keeping the uploaded data?","title":"Questions and answers","text":"! uploaded data deleted session ends, stored analyses immediately deleted.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/ROADMAP.html","id":null,"dir":"","previous_headings":"","what":"Project roadmap","title":"Project roadmap","text":"current state app considered experimental, lot things still changing. , however, usable state, basic functions available user. (actual list quite long growing) planned features improvements: Stratified analyses Additional study designs: Cross-sectional data analyses Longitudinal data analyses Survival analysis detailed variable browser Add histograms data distribution. 2025-01-16 Option edit labels. 2025-01-16 output controls Theming output tables Select analyses include report Export modified data. 2025-01-16 Include reproducible code steps (maybe , steps, final dataset can exported) Modify factor levels Factor level modifications possible converting factors numeric > cutting numeric desired fixed values. 2024-12-12 options date/datetime/time grouping/factoring. Included weekday month-options. 2024-12-12 Graphs plots Correlation matrix plot data exploration 2025-2-20 Grotta bars ordianl outcomes Coefficient plotting regression analyses (forest plot) 2025-2-20","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andreas Gammelgaard Damsbo. Author, maintainer.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo (2025). freesearcheR: Browser Based Data Analysis. R package version 25.3.1, https://agdamsbo.github.io/freesearcheR/, https://github.com/agdamsbo/freesearcheR.","code":"@Manual{,   title = {freesearcheR: Browser Based Data Analysis},   author = {Andreas Gammelgaard Damsbo},   year = {2025},   note = {R package version 25.3.1, https://agdamsbo.github.io/freesearcheR/},   url = {https://github.com/agdamsbo/freesearcheR}, }"},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"freesearcher","dir":"","previous_headings":"","what":"Browser Based Data Analysis","title":"Browser Based Data Analysis","text":"package backbone freesearcheR, free open-source browser based data exploration analysis tool clinicians researchers publication ready output. package freesearcheR-tool part larger initiative democratize health data analysis remove barriers clinicians engage health research. freesearcheR-tool online accessible : link app freely hosted shinyapps.io. feedback welcome can shared GitHub issue. Initiatives funding continued development tool surrounding initiatives ongoing.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"install-locally","dir":"","previous_headings":"","what":"Install locally","title":"Browser Based Data Analysis","text":"freesearcheR-tool can also launched locally. data.frame available global environment accessible interface.","code":"require(\"devtools\") devtools::install_github(\"agdamsbo/freesearcheR\") library(freesearcheR) # By loading mtcars to the environment, it will be available # in the interface like any other data.frame data(mtcars) shiny_freesearcheR()"},{"path":"https://agdamsbo.github.io/freesearcheR/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Browser Based Data Analysis","text":"Please note freesearcheR project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert class grid column to icon — add_class_icon","title":"Convert class grid column to icon — add_class_icon","text":"Convert class grid column icon","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert class grid column to icon — add_class_icon","text":"","code":"add_class_icon(grid, column = \"class\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert class grid column to icon — add_class_icon","text":"grid grid column column","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert class grid column to icon — add_class_icon","text":"datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_class_icon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert class grid column to icon — add_class_icon","text":"","code":"mtcars |>   overview_vars() |>   toastui::datagrid() |>   add_class_icon()      {\"x\":{\"nrow\":11,\"ncol\":7,\"data\":[[\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\"],[\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\",\"numeric\"],[\"mpg\",\"cyl\",\"disp\",\"hp\",\"drat\",\"wt\",\"qsec\",\"vs\",\"am\",\"gear\",\"carb\"],[0,0,0,0,0,0,0,0,0,0,0],[1,1,1,1,1,1,1,1,1,1,1],[25,3,27,22,22,29,30,2,2,3,6],[[21,21,22.8,21.4,18.7,18.1,14.3,24.4,22.8,19.2,17.8,16.4,17.3,15.2,10.4,10.4,14.7,32.4,30.4,33.9,21.5,15.5,15.2,13.3,19.2,27.3,26,30.4,15.8,19.7,15,21.4],[6,6,4,6,8,6,8,4,4,6,6,8,8,8,8,8,8,4,4,4,4,8,8,8,8,4,4,4,8,6,8,4],[160,160,108,258,360,225,360,146.7,140.8,167.6,167.6,275.8,275.8,275.8,472,460,440,78.7,75.7,71.09999999999999,120.1,318,304,350,400,79,120.3,95.09999999999999,351,145,301,121],[110,110,93,110,175,105,245,62,95,123,123,180,180,180,205,215,230,66,52,65,97,150,150,245,175,66,91,113,264,175,335,109],[3.9,3.9,3.85,3.08,3.15,2.76,3.21,3.69,3.92,3.92,3.92,3.07,3.07,3.07,2.93,3,3.23,4.08,4.93,4.22,3.7,2.76,3.15,3.73,3.08,4.08,4.43,3.77,4.22,3.62,3.54,4.11],[2.62,2.875,2.32,3.215,3.44,3.46,3.57,3.19,3.15,3.44,3.44,4.07,3.73,3.78,5.25,5.424,5.345,2.2,1.615,1.835,2.465,3.52,3.435,3.84,3.845,1.935,2.14,1.513,3.17,2.77,3.57,2.78],[16.46,17.02,18.61,19.44,17.02,20.22,15.84,20,22.9,18.3,18.9,17.4,17.6,18,17.98,17.82,17.42,19.47,18.52,19.9,20.01,16.87,17.3,15.41,17.05,18.9,16.7,16.9,14.5,15.5,14.6,18.6],[0,0,1,1,0,1,0,1,1,1,1,0,0,0,0,0,0,1,1,1,1,0,0,0,0,1,0,1,0,0,0,1],[1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,1,1,1,1,1,1,1],[4,4,4,3,3,3,3,4,4,4,4,3,3,3,3,3,3,4,4,4,3,3,3,3,3,4,5,5,5,5,5,4],[4,4,1,1,2,1,4,2,2,4,4,3,3,3,4,4,4,1,2,1,1,2,2,4,2,1,2,2,4,6,8,2]]],\"colnames\":[\"class\",\"type\",\"name\",\"n_missing\",\"p_complete\",\"n_unique\",\"vals\"],\"options\":{\"columns\":[{\"header\":\"class\",\"name\":\"class\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"},\"type\":\"datagrid.renderer.format\",\"options\":{\"formatted\":[\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\",\"<i class=\\\"fas fa-calculator\\\" role=\\\"presentation\\\" aria-label=\\\"calculator icon\\\"><\\/i>\"]}},\"width\":60},{\"header\":\"type\",\"name\":\"type\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"name\",\"name\":\"name\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"n_missing\",\"name\":\"n_missing\",\"sortable\":true,\"align\":\"right\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"p_complete\",\"name\":\"p_complete\",\"sortable\":true,\"align\":\"right\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"n_unique\",\"name\":\"n_unique\",\"sortable\":true,\"align\":\"right\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}},{\"header\":\"vals\",\"name\":\"vals\",\"sortable\":true,\"align\":\"left\",\"whiteSpace\":\"normal\",\"renderer\":{\"styles\":{\"wordBreak\":\"normal\"}}}],\"bodyHeight\":\"fitToParent\",\"draggable\":false,\"usageStatistics\":false,\"contextMenu\":null,\"rowHeight\":\"auto\"},\"theme\":\"clean\",\"themeOptions\":{\"cell\":{\"normal\":{\"showHorizontalBorder\":true}}},\"language\":\"en\",\"languageOptions\":[],\"filters\":false,\"rowAttributes\":[],\"validationInput\":false,\"dataAsInput\":false,\"dragInput\":false},\"evals\":[\"options.columns.0.renderer.type\"],\"jsHooks\":[]}"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_sparkline.html","id":null,"dir":"Reference","previous_headings":"","what":"Add sparkline to datagrid — add_sparkline","title":"Add sparkline to datagrid — add_sparkline","text":"Add sparkline datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_sparkline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add sparkline to datagrid — add_sparkline","text":"","code":"add_sparkline(   grid,   column = \"vals\",   color.main = \"#2a8484\",   color.sec = \"#84EF84\" )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_sparkline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add sparkline to datagrid — add_sparkline","text":"grid grid column clumn transform","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_sparkline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add sparkline to datagrid — add_sparkline","text":"datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/add_sparkline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add sparkline to datagrid — add_sparkline","text":"","code":"grid <- mtcars |>   default_parsing() |>   overview_vars() |>   toastui::datagrid() |>   add_sparkline() grid      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theme based on unity — custom_theme","title":"Custom theme based on unity — custom_theme","text":"Custom theme based unity","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/custom_theme.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom theme based on unity — custom_theme","text":"","code":"custom_theme(   ...,   version = 5,   primary = \"#1E4A8F\",   secondary = \"#FF6F61\",   bootswatch = \"united\",   base_font = bslib::font_google(\"Montserrat\"),   heading_font = bslib::font_google(\"Public Sans\", wght = \"700\"),   code_font = bslib::font_google(\"Open Sans\") )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/custom_theme.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom theme based on unity — custom_theme","text":"... everything passed bslib::bs_theme()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/custom_theme.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom theme based on unity — custom_theme","text":"theme list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":null,"dir":"Reference","previous_headings":"","what":"Module to Convert Numeric to Factor — cut-variable","title":"Module to Convert Numeric to Factor — cut-variable","text":"module contain interface cut numeric several intervals.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module to Convert Numeric to Factor — cut-variable","text":"","code":"cut_variable_ui(id)  cut_variable_server(id, data_r = reactive(NULL))  modal_cut_variable(   id,   title = i18n(\"Convert Numeric to Factor\"),   easyClose = TRUE,   size = \"l\",   footer = NULL )  winbox_cut_variable(   id,   title = i18n(\"Convert Numeric to Factor\"),   options = shinyWidgets::wbOptions(),   controls = shinyWidgets::wbControls() )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/cut-variable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module to Convert Numeric to Factor — cut-variable","text":"id Module ID. data_r shiny::reactive() function returning data.frame. title optional title dialog. easyClose TRUE, modal dialog can dismissed clicking outside dialog box, pressing Escape key. 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returning \"UTC\". #> [1] 01:00:20 02:10:20 01:00:20 02:10:20 <NA>     #> attr(,\"brks\") #> 01:00:20 #> 02:10:20 #> 03:02:21 #> Levels: 01:00:20 02:10:20 readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(2) #> [1] 1992-02-01 01:00:20 1992-02-01 01:00:20 1992-02-01 01:00:20 #> [4] 1992-02-01 01:00:20 1999-02-01 21:20:20 1992-02-01 01:00:20 #> Levels: 1992-02-01 01:00:20 1999-02-01 21:20:20 readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"weekday\") #> Error in cut.POSIXt(readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"weekday\"): invalid specification of 'breaks' readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"month_only\") #> Error in cut.POSIXt(readr::parse_datetime(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"month_only\"): invalid specification of 'breaks' as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(2) #> [1] 1992-02-01 1992-02-01 1992-02-01 1992-02-01 1999-02-01 1992-02-01 #> Levels: 1992-02-01 1999-02-01 as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\", \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\", \"1992-12-01 03:02:20\")) |> cut(breaks=\"weekday\") #> Error in cut.Date(as.Date(c(\"1992-02-01 01:00:20\", \"1992-02-06 03:00:20\",     \"1992-05-01 01:20:20\", \"1992-09-01 08:20:20\", \"1999-02-01 21:20:20\",     \"1992-12-01 03:02:20\")), breaks = \"weekday\"): invalid specification of 'breaks'"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":null,"dir":"Reference","previous_headings":"","what":"Data correlations evaluation module — data-correlations","title":"Data correlations evaluation module — data-correlations","text":"Data correlations evaluation module Data correlations evaluation module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data correlations evaluation module — data-correlations","text":"","code":"data_correlations_ui(id, ...)  data_correlations_server(id, data, include.class = NULL, cutoff = 0.7, ...)  data_visuals_ui(id, tab_title = \"Plots\", ...)  data_visuals_server(id, data, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data correlations evaluation module — data-correlations","text":"id Module id. (Use 'ns(\"id\")') ... ignored data data color.main main color color.sec secondary color","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-correlations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data correlations evaluation module — data-correlations","text":"Shiny ui module shiny server module Shiny ui module shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Title — data-plots","title":"Title — data-plots","text":"Title Wrapper create plot based provided type Nice horizontal stacked bars (Grotta bars) Beatiful violin plot Beautiful violin plot Beautiful sankey plot option split tertiary group","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title — data-plots","text":"","code":"plot_ridge(data, x, y, z = NULL, ...)  create_plot(data, type, x, y, z = NULL, ...)  plot_hbars(data, x, y, z = NULL)  plot_violin(data, x, y, z = NULL)  plot_scatter(data, x, y, z = NULL)  plot_sankey(data, x, y, z = NULL, color.group = \"x\", colors = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title — data-plots","text":"... ignored now type plot type (derived possible_plots() matches custom function)","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title — data-plots","text":"ggplot2 object ggplot2 object ggplot2 object ggplot2 object ggplot2 object ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Title — data-plots","text":"","code":"mtcars |>   default_parsing() |>   plot_ridge(x = \"mpg\", y = \"cyl\") #> Picking joint bandwidth of 1.38  mtcars |> plot_ridge(x = \"mpg\", y = \"cyl\", z = \"gear\") #> Picking joint bandwidth of 1.52 #> Warning: The following aesthetics were dropped during statistical transformation: y and #> fill. #> ℹ This can happen when ggplot fails to infer the correct grouping structure in #>   the data. #> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical #>   variable into a factor? #> Error in ggridges::geom_density_ridges(): Problem while setting up geom. #> ℹ Error occurred in the 1st layer. #> Caused by error in `compute_geom_1()`: #> ! `geom_density_ridges()` requires the following missing aesthetics: y. create_plot(mtcars, \"plot_violin\", \"mpg\", \"cyl\") #> Error in if (!z %in% names(data)) {    z <- NULL}: argument is of length zero mtcars |> plot_hbars(x = \"carb\", y = \"cyl\") #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale.  mtcars |> plot_hbars(x = \"carb\", y = NULL) #> Scale for fill is already present. #> Adding another scale for fill, which will replace the existing scale.  mtcars |> plot_violin(x = \"mpg\", y = \"cyl\", z = \"gear\") #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 1: `cyl = 4`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 1: `cyl = 4`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 2: `cyl = 6`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: There was 1 warning in `summarize()`. #> ℹ In argument: `V1 = .fun(as.data.frame(pick(everything())), var)`. #> ℹ In group 2: `cyl = 6`. #> Caused by warning in `stats::qt()`: #> ! NaNs produced #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes. #> Warning: Groups with fewer than two datapoints have been dropped. #> ℹ Set `drop = FALSE` to consider such groups for position adjustment purposes.  mtcars |> plot_scatter(x = \"mpg\", y = \"wt\")  ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) ds |> plot_sankey(\"first\", \"last\") #> Loading required package: ggplot2  ds |> plot_sankey(\"first\", \"last\", color.group = \"y\")  ds |> plot_sankey(\"first\", \"last\", z = \"g\", color.group = \"y\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":null,"dir":"Reference","previous_headings":"","what":"Data summary module — data-summary","title":"Data summary module — data-summary","text":"Data summary module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data summary module — data-summary","text":"","code":"data_summary_ui(id)  data_summary_server(id, data, color.main, color.sec, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data summary module — data-summary","text":"id Module id. (Use 'ns(\"id\")') data data color.main main color color.sec secondary color ... arguments passed toastui::datagrid","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/data-summary.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data summary module — data-summary","text":"Shiny ui module shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Defaults qmd formats — default_format_arguments","title":"Defaults qmd formats — default_format_arguments","text":"Defaults qmd formats","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Defaults qmd formats — default_format_arguments","text":"","code":"default_format_arguments()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_format_arguments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Defaults qmd formats — default_format_arguments","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":null,"dir":"Reference","previous_headings":"","what":"Default data parsing — default_parsing","title":"Default data parsing — default_parsing","text":"Default data parsing","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default data parsing — default_parsing","text":"","code":"default_parsing(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default data parsing — default_parsing","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default data parsing — default_parsing","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/default_parsing.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Default data parsing — default_parsing","text":"","code":"mtcars |> str() #> 'data.frame':\t32 obs. of  11 variables: #>  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num  160 160 108 258 360 ... #>  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num  16.5 17 18.6 19.4 17 ... #>  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num  1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num  4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num  4 4 1 1 2 1 4 2 2 4 ... mtcars |>   default_parsing() |>   str() #> tibble [32 × 11] (S3: tbl_df/tbl/data.frame) #>  $ mpg : num [1:32] 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : Factor w/ 3 levels \"4\",\"6\",\"8\": 2 2 1 2 3 2 3 1 1 2 ... #>  $ disp: num [1:32] 160 160 108 258 360 ... #>  $ hp  : num [1:32] 110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num [1:32] 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num [1:32] 2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num [1:32] 16.5 17 18.6 19.4 17 ... #>  $ vs  : Factor w/ 2 levels \"0\",\"1\": 1 1 2 2 1 2 1 2 2 2 ... #>  $ am  : Factor w/ 2 levels \"0\",\"1\": 2 2 2 1 1 1 1 1 1 1 ... #>  $ gear: Factor w/ 3 levels \"3\",\"4\",\"5\": 2 2 2 1 1 1 1 2 2 2 ... #>  $ carb: Factor w/ 6 levels \"1\",\"2\",\"3\",\"4\",..: 4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":null,"dir":"Reference","previous_headings":"","what":"Factorize variables in data.frame — factorize","title":"Factorize variables in data.frame — factorize","text":"Factorize variables data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Factorize variables in data.frame — factorize","text":"","code":"factorize(data, vars)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Factorize variables in data.frame — factorize","text":"data data.frame vars variables force factorize","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/factorize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Factorize variables in data.frame — factorize","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":null,"dir":"Reference","previous_headings":"","what":"Title — file_export","title":"Title — file_export","text":"Title","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title — file_export","text":"","code":"file_export(data, output.format = c(\"df\", \"teal\", \"list\"), filename, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title — file_export","text":"data data output.format output filename filename ... passed ","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/file_export.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Title — file_export","text":"data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":null,"dir":"Reference","previous_headings":"","what":"Merges list of named arguments for qmd header generation — format_writer","title":"Merges list of named arguments for qmd header generation — format_writer","text":"Merges list named arguments qmd header generation","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merges list of named arguments for qmd header generation — format_writer","text":"","code":"format_writer(data, name)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merges list of named arguments for qmd header generation — format_writer","text":"data vector name name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/format_writer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merges list of named arguments for qmd header generation — format_writer","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the function options based on the selected function description — get_fun_options","title":"Get the function options based on the selected function description — get_fun_options","text":"Get function options based selected function description","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the function options based on the selected function description — get_fun_options","text":"","code":"get_fun_options(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the function options based on the selected function description — get_fun_options","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the function options based on the selected function description — get_fun_options","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_fun_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the function options based on the selected function description — get_fun_options","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(mpg) |>   possible_functions(design = \"cross-sectional\") |>   (\\(.x){     .x[[1]]   })() |>   get_fun_options() #> $lm #> $lm$descr #> [1] \"Linear regression model\" #>  #> $lm$design #> [1] \"cross-sectional\" #>  #> $lm$out.type #> [1] \"continuous\" #>  #> $lm$fun #> [1] \"stats::lm\" #>  #> $lm$args.list #> NULL #>  #> $lm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $lm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $lm$table.args.list #> $lm$table.args.list$exponentiate #> [1] FALSE #>  #>  #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Print label, and if missing print variable name — get_label","title":"Print label, and if missing print variable name — get_label","text":"Print label, missing print variable name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print label, and if missing print variable name — get_label","text":"","code":"get_label(data, var = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print label, and if missing print variable name — get_label","text":"data vector data 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get_plot_options","title":"Get the function options based on the selected function description — get_plot_options","text":"Get function options based selected function description","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the function options based on the selected function description — get_plot_options","text":"","code":"get_plot_options(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the function options based on the selected function description — get_plot_options","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the function options based on the selected function description — get_plot_options","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/get_plot_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the function options based on the selected function description — get_plot_options","text":"","code":"ls <- mtcars |>   default_parsing() |>   dplyr::pull(mpg) |>   possible_plots() |>   (\\(.x){     .x[[1]]   })() |>   get_plot_options()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"function follows idea comment: https://stackoverflow.com/questions/38983179/-call--function--r-without-loading--package","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"","code":"getfun(x)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"x function function name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"function character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/getfun.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrapper function to get function from character vector referring to function from namespace. Passed to 'do.call()' — getfun","text":"","code":"getfun(\"stats::lm\") #> function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> } #> <bytecode: 0x556a34cd2538> #> <environment: namespace:stats>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":null,"dir":"Reference","previous_headings":"","what":"GGplot default theme for plotting export objects — gg_theme_export","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"GGplot default theme plotting export objects","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"","code":"gg_theme_export()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_export.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GGplot default theme for plotting export objects — gg_theme_export","text":"data ggplot 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gg_theme_shiny","text":"","code":"gg_theme_shiny()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"data ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/gg_theme_shiny.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"GGplot default theme for plotting in Shiny — gg_theme_shiny","text":"ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/index_embed.html","id":null,"dir":"Reference","previous_headings":"","what":"Split vector by an index and embed addition — index_embed","title":"Split vector by an index and embed addition — index_embed","text":"Split vector index embed 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class — is_any_class","text":"Test class","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test class — is_any_class","text":"","code":"is_any_class(data, class.vec)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test class — is_any_class","text":"data data class.vec vector class names test","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test class — is_any_class","text":"factor","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_any_class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test class — is_any_class","text":"","code":"if (FALSE) { # \\dontrun{ vapply(REDCapCAST::redcapcast_data, \\(.x){   is_any_class(.x, c(\"hms\", \"Date\", \"POSIXct\", \"POSIXt\")) }, logical(1)) } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"Checks elements vector equally spaced indication ID","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"","code":"is_consecutive(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"logical","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_consecutive.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checks if elements in vector are equally spaced as indication of ID — is_consecutive","text":"","code":"1:10 |> is_consecutive() #> [1] TRUE sample(1:100,40) |> is_consecutive() #> [1] FALSE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":null,"dir":"Reference","previous_headings":"","what":"Test is date/datetime/time — is_datetime","title":"Test is date/datetime/time — is_datetime","text":"Test date/datetime/time","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test is date/datetime/time — is_datetime","text":"","code":"is_datetime(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test is date/datetime/time — is_datetime","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test is date/datetime/time — is_datetime","text":"factor","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_datetime.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test is date/datetime/time — is_datetime","text":"","code":"vapply(REDCapCAST::redcapcast_data, is_datetime, logical(1)) #>                    record_id            redcap_event_name  #>                        FALSE                        FALSE  #>     redcap_repeat_instrument       redcap_repeat_instance  #>                        FALSE                        FALSE  #>                          cpr                    inclusion  #>                        FALSE                         TRUE  #>               inclusion_time                          dob  #>                         TRUE                         TRUE  #>                          age                  age_integer  #>                        FALSE                        FALSE  #>                          sex                 cohabitation  #>                        FALSE                        FALSE  #>                 hypertension                     diabetes  #>                        FALSE                        FALSE  #>                       region baseline_data_start_complete  #>                        FALSE                        FALSE  #>                 mrs_assessed                     mrs_date  #>                        FALSE                         TRUE  #>                    mrs_score                 mrs_complete  #>                        FALSE                        FALSE  #>                      con_mrs                     con_calc  #>                        FALSE                        FALSE  #>           consensus_complete               event_datetime  #>                        FALSE                         TRUE  #>                    event_age                   event_type  #>                        FALSE                        FALSE  #>           new_event_complete  #>                        FALSE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":null,"dir":"Reference","previous_headings":"","what":"Title — is_valid_redcap_url","title":"Title — is_valid_redcap_url","text":"Title","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Title — is_valid_redcap_url","text":"","code":"is_valid_redcap_url(url)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Title — is_valid_redcap_url","text":"url","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_redcap_url.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Title — is_valid_redcap_url","text":"","code":"url <- c(   \"www.example.com\",   \"http://example.com\",   \"https://redcap.your.inst/api/\" ) is_valid_redcap_url(url) #> [1] FALSE FALSE  TRUE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate REDCap token — is_valid_token","title":"Validate REDCap token — is_valid_token","text":"Validate REDCap token","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate REDCap token — is_valid_token","text":"","code":"is_valid_token(token, pattern_env = NULL, nchar = 32)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate REDCap token — is_valid_token","text":"token token pattern_env pattern","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/is_valid_token.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate REDCap token — is_valid_token","text":"","code":"token <- paste(sample(c(1:9, LETTERS[1:6]), 32, TRUE), collapse = \"\") is_valid_token(token) #> [1] TRUE"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily launch the freesearcheR app — launch_freesearcheR","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"Easily launch freesearcheR app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"","code":"launch_freesearcheR(...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"... passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/launch_freesearcheR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily launch the freesearcheR app — launch_freesearcheR","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":null,"dir":"Reference","previous_headings":"","what":"Line breaking at given number of characters for nicely plotting labels — line_break","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"Line breaking given number characters nicely plotting labels","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"","code":"line_break(data, lineLength = 20)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/line_break.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Line breaking at given number of characters for nicely plotting labels — line_break","text":"lineLength","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny UI module to load a data file — m_datafileUI","title":"Shiny UI module to load a data file — m_datafileUI","text":"Shiny UI module load data file","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny UI module to load a data file — m_datafileUI","text":"","code":"m_datafileUI(id)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny UI module to load a data file — m_datafileUI","text":"id id","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/m_datafileUI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny UI module to load a data file — m_datafileUI","text":"shiny UI","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"Wrapper pivot gtsummary table data long plotting","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"","code":"merge_long(list, model.names)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"list custom regression models list model.names names models include","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/merge_long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to pivot gtsummary table data to long for plotting — merge_long","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to modify quarto file to render specific formats — modify_qmd","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"Wrapper modify quarto file render specific formats","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"","code":"modify_qmd(file, format)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"file filename format desired output","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/modify_qmd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to modify quarto file to render specific formats — modify_qmd","text":"none","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Outcome data type assessment — outcome_type","title":"Outcome data type assessment — outcome_type","text":"Outcome data type assessment","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Outcome data type assessment — outcome_type","text":"","code":"outcome_type(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Outcome data type assessment — outcome_type","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Outcome data type assessment — outcome_type","text":"outcome type","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/outcome_type.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Outcome data type assessment — outcome_type","text":"","code":"mtcars |>   default_parsing() |>   lapply(outcome_type) #> $mpg #> [1] \"continuous\" #>  #> $cyl #> [1] \"ordinal\" #>  #> $disp #> [1] \"continuous\" #>  #> $hp #> [1] \"continuous\" #>  #> $drat #> [1] \"continuous\" #>  #> $wt #> [1] \"continuous\" #>  #> $qsec #> [1] \"continuous\" #>  #> $vs #> [1] \"dichotomous\" #>  #> $am #> [1] \"dichotomous\" #>  #> $gear #> [1] \"ordinal\" #>  #> $carb #> [1] \"ordinal\" #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a data overview data.frame ready for sparklines — overview_vars","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"Create data overview data.frame ready sparklines","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"","code":"overview_vars(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/overview_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a data overview data.frame ready for sparklines — overview_vars","text":"","code":"mtcars |> overview_vars() #> # A tibble: 11 × 7 #>    class   type    name  n_missing p_complete n_unique vals         #>    <chr>   <chr>   <chr>     <dbl>      <dbl>    <int> <named list> #>  1 numeric numeric mpg           0          1       25 <dbl [32]>   #>  2 numeric numeric cyl           0          1        3 <dbl [32]>   #>  3 numeric numeric disp          0          1       27 <dbl [32]>   #>  4 numeric numeric hp            0          1       22 <dbl [32]>   #>  5 numeric numeric drat          0          1       22 <dbl [32]>   #>  6 numeric numeric wt            0          1       29 <dbl [32]>   #>  7 numeric numeric qsec          0          1       30 <dbl [32]>   #>  8 numeric numeric vs            0          1        2 <dbl [32]>   #>  9 numeric numeric am            0          1        2 <dbl [32]>   #> 10 numeric numeric gear          0          1        3 <dbl [32]>   #> 11 numeric numeric carb          0          1        6 <dbl [32]>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"Regression coef plot gtsummary. Slightly modified pass arguments","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"","code":"# S3 method for class 'tbl_regression' plot(x, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"x (tbl_regression, tbl_uvregression) 'tbl_regression' 'tbl_uvregression' object ... arguments passed ggstats::ggcoef_plot(...)","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"ggplot object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot.tbl_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Regression coef plot from gtsummary. Slightly modified to pass on arguments — plot.tbl_regression","text":"","code":"if (FALSE) { # \\dontrun{ mod <- lm(mpg ~ ., mtcars) p <- mod |>   gtsummary::tbl_regression() |>   plot(colour = \"variable\") } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":null,"dir":"Reference","previous_headings":"","what":"Beautiful sankey plot — plot_sankey_single","title":"Beautiful sankey plot — plot_sankey_single","text":"Beautiful sankey plot","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Beautiful sankey plot — plot_sankey_single","text":"","code":"plot_sankey_single(data, x, y, color.group = \"x\", colors = NULL)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Beautiful sankey plot — plot_sankey_single","text":"colors","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Beautiful sankey plot — plot_sankey_single","text":"ggplot2 object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/plot_sankey_single.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Beautiful sankey plot — plot_sankey_single","text":"","code":"ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE))) ds |> plot_sankey_single(\"first\", \"last\")  ds |> plot_sankey_single(\"first\", \"last\", color.group = \"y\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Get possible regression models — possible_functions","title":"Get possible regression models — possible_functions","text":"Get possible regression models","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get possible regression models — possible_functions","text":"","code":"possible_functions(data, design = c(\"cross-sectional\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get possible regression models — possible_functions","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get possible regression models — possible_functions","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get possible regression models — possible_functions","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(\"cyl\") |>   possible_functions(design = \"cross-sectional\") #> [1] \"Ordinal logistic regression model\"  mtcars |>   default_parsing() |>   dplyr::select(\"cyl\") |>   possible_functions(design = \"cross-sectional\") #> [1] \"Ordinal logistic regression model\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Get possible regression models — possible_plots","title":"Get possible regression models — possible_plots","text":"Get possible regression models","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get possible regression models — possible_plots","text":"","code":"possible_plots(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get possible regression models — possible_plots","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get possible regression models — possible_plots","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/possible_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get possible regression models — possible_plots","text":"","code":"mtcars |>   default_parsing() |>   dplyr::pull(\"cyl\") |>   possible_plots() #> [1] \"Stacked horizontal bars\" \"Violin plot\"             #> [3] \"Sankey plot\"              mtcars |>   default_parsing() |>   dplyr::select(\"mpg\") |>   possible_plots() #> [1] \"Violin plot\"  \"Ridge plot\"   \"Scatter plot\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Flexible file import based on extension — read_input","title":"Flexible file import based on extension — read_input","text":"Flexible file import based extension","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(file, consider.na = c(\"NA\", \"\\\"\\\"\", \"\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flexible file import based on extension — read_input","text":"file file name consider.na character vector strings consider NAs","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Flexible file import based on extension — read_input","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/read_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(\"https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv\") #> Rows: 28 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> dbl (8): id, ab, age, imm, vis, ver, att, del #>  #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> # A tibble: 28 × 8 #>       id    ab   age   imm   vis   ver   att   del #>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1     1     1    74    38    35    30    29    35 #>  2     1     2    69    36    36    21    27    37 #>  3     2     1    63    32    31    26    34    38 #>  4     2     2    64    37    34    26    36    46 #>  5     3     1    69    39    33    31    47    29 #>  6     3     2    70    40    36    31    46    25 #>  7     4     1    79    44    37    20    37    36 #>  8     4     2    81    35    36    31    37    40 #>  9     5     1    77    35    26    17    20    36 #> 10     5     2    80    29    34    18    23    36 #> # ℹ 18 more rows"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny module to browser and export REDCap data — m_redcap_readUI","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"Shiny module browser export REDCap data Test app redcap_read_shiny_module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"","code":"m_redcap_readUI(id, include_title = TRUE)  m_redcap_readServer(id)  redcap_demo_app()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"id Namespace id include_title logical include title","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"shiny ui element shiny server module","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/redcap_read_shiny_module.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Shiny module to browser and export REDCap data — m_redcap_readUI","text":"","code":"if (FALSE) { # \\dontrun{ redcap_demo_app() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a regression model programatically — regression_model","title":"Create a regression model programatically — regression_model","text":"Output concatenated list model information model","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a regression model programatically — regression_model","text":"","code":"regression_model(   data,   outcome.str,   auto.mode = FALSE,   formula.str = NULL,   args.list = NULL,   fun = NULL,   vars = NULL,   ... )  regression_model_uv(   data,   outcome.str,   args.list = NULL,   fun = NULL,   vars = NULL,   ... )  regression_model_list(   data,   outcome.str,   fun.descr,   fun = NULL,   formula.str = NULL,   args.list = NULL,   vars = NULL,   ... )  regression_model_uv_list(   data,   outcome.str,   fun.descr,   fun = NULL,   formula.str = NULL,   args.list = NULL,   vars = NULL,   ... )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a regression model programatically — regression_model","text":"data data outcome.str name outcome variable auto.mode Make assumptions function dependent outcome data format. Overwrites arguments. formula.str custom formula glue string. Default NULL. args.list custom character string converted using argsstring2list() list arguments. Default NULL. fun name custom function. Default NULL. vars character vector variables include ... ignored fun.descr Description chosen function matching description \"supported_functions()\"","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a regression model programatically — regression_model","text":"object standard class fun object standard class fun list list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_model.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a regression model programatically — regression_model","text":"","code":"gtsummary::trial |>   regression_model(outcome.str = \"age\") #>  #> Call: #> (function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> })(formula = age ~ trt + marker + stage + grade + response +  #>     death + ttdeath, data = structure(list(trt = structure(c(1L,  #> 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L,  #> 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L,  #> 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #> 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L,  #> 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L,  #> 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L,  #> 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L,  #> 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,  #> 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\", \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(0L,  #>     1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L,  #>     0L, 0L, 1L, 0L, NA, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     0L, 0L, 0L, NA, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     1L, 1L, NA, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, NA, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 0L,  #>     0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, NA, 0L, 1L,  #>     0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L,  #>     1L, 1L, 0L, 0L), label = \"Tumor Response\"), death = structure(c(0L,  #>     0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L,  #>     0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L,  #>     1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L,  #>     1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L,  #>     1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L,  #>     0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 1L, 0L), label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)    trtDrug B       marker      stageT2      stageT3      stageT4   #>     45.9247      -0.4052      -0.1435       2.0519       2.4437      -3.1573   #>     gradeII     gradeIII     response        death      ttdeath   #>      0.1750       1.6855       4.9885       3.0775      -0.1394   #>  gtsummary::trial |>   regression_model(     outcome.str = \"age\",     auto.mode = FALSE,     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) #>  #> Call: #> (function (formula, data, subset, weights, na.action, method = \"qr\",  #>     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, offset, ...)  #> { #>     ret.x <- x #>     ret.y <- y #>     cl <- match.call() #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (method == \"model.frame\")  #>         return(mf) #>     else if (method != \"qr\")  #>         warning(gettextf(\"method = '%s' is not supported. Using 'qr'\",  #>             method), domain = NA) #>     mt <- attr(mf, \"terms\") #>     y <- model.response(mf, \"numeric\") #>     w <- as.vector(model.weights(mf)) #>     if (!is.null(w) && !is.numeric(w))  #>         stop(\"'weights' must be a numeric vector\") #>     offset <- model.offset(mf) #>     mlm <- is.matrix(y) #>     ny <- if (mlm)  #>         nrow(y) #>     else length(y) #>     if (!is.null(offset)) { #>         if (!mlm)  #>             offset <- as.vector(offset) #>         if (NROW(offset) != ny)  #>             stop(gettextf(\"number of offsets is %d, should equal %d (number of observations)\",  #>                 NROW(offset), ny), domain = NA) #>     } #>     if (is.empty.model(mt)) { #>         x <- NULL #>         z <- list(coefficients = if (mlm) matrix(NA_real_, 0,  #>             ncol(y)) else numeric(), residuals = y, fitted.values = 0 *  #>             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=  #>             0) else ny) #>         if (!is.null(offset)) { #>             z$fitted.values <- offset #>             z$residuals <- y - offset #>         } #>     } #>     else { #>         x <- model.matrix(mt, mf, contrasts) #>         z <- if (is.null(w))  #>             lm.fit(x, y, offset = offset, singular.ok = singular.ok,  #>                 ...) #>         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,  #>             ...) #>     } #>     class(z) <- c(if (mlm) \"mlm\", \"lm\") #>     z$na.action <- attr(mf, \"na.action\") #>     z$offset <- offset #>     z$contrasts <- attr(x, \"contrasts\") #>     z$xlevels <- .getXlevels(mt, mf) #>     z$call <- cl #>     z$terms <- mt #>     if (model)  #>         z$model <- mf #>     if (ret.x)  #>         z$x <- x #>     if (ret.y)  #>         z$y <- y #>     if (!qr)  #>         z$qr <- NULL #>     z #> })(formula = age ~ ., data = structure(list(trt = structure(c(1L,  #> 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L,  #> 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L,  #> 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L,  #> 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #> 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L,  #> 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L,  #> 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #> 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L,  #> 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 1L,  #> 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L,  #> 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\", \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(0L,  #>     1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L,  #>     0L, 0L, 1L, 0L, NA, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     0L, 0L, 0L, NA, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L,  #>     0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L,  #>     1L, 1L, NA, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, NA, 1L, 0L,  #>     0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 0L,  #>     0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, NA, 0L, 1L,  #>     0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L,  #>     1L, 1L, 0L, 0L), label = \"Tumor Response\"), death = structure(c(0L,  #>     0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L,  #>     0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  #>     0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L,  #>     1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L,  #>     1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L,  #>     1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L,  #>     0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L,  #>     0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L,  #>     0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L,  #>     1L, 0L, 1L, 0L), label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)    trtDrug B       marker      stageT2      stageT3      stageT4   #>     45.9247      -0.4052      -0.1435       2.0519       2.4437      -3.1573   #>     gradeII     gradeIII     response        death      ttdeath   #>      0.1750       1.6855       4.9885       3.0775      -0.1394   #>  gtsummary::trial |>   default_parsing() |>   regression_model(     outcome.str = \"trt\",     auto.mode = FALSE,     fun = \"stats::glm\",     args.list = list(family = binomial(link = \"logit\"))   ) #>  #> Call:  (function (formula, family = gaussian, data, weights, subset,  #>     na.action, start = NULL, etastart, mustart, offset, control = list(...),  #>     model = TRUE, method = \"glm.fit\", x = FALSE, y = TRUE, singular.ok = TRUE,  #>     contrasts = NULL, ...)  #> { #>     cal <- match.call() #>     if (is.character(family))  #>         family <- get(family, mode = \"function\", envir = parent.frame()) #>     if (is.function(family))  #>         family <- family() #>     if (is.null(family$family)) { #>         print(family) #>         stop(\"'family' not recognized\") #>     } #>     if (missing(data))  #>         data <- environment(formula) #>     mf <- match.call(expand.dots = FALSE) #>     m <- match(c(\"formula\", \"data\", \"subset\", \"weights\", \"na.action\",  #>         \"etastart\", \"mustart\", \"offset\"), names(mf), 0L) #>     mf <- mf[c(1L, m)] #>     mf$drop.unused.levels <- TRUE #>     mf[[1L]] <- quote(stats::model.frame) #>     mf <- eval(mf, parent.frame()) #>     if (identical(method, \"model.frame\"))  #>         return(mf) #>     if (!is.character(method) && !is.function(method))  #>         stop(\"invalid 'method' argument\") #>     if (identical(method, \"glm.fit\"))  #>         control <- do.call(\"glm.control\", control) #>     mt <- attr(mf, \"terms\") #>     Y <- model.response(mf, \"any\") #>     if (length(dim(Y)) == 1L) { #>         nm <- rownames(Y) #>         dim(Y) <- NULL #>         if (!is.null(nm))  #>             names(Y) <- nm #>     } #>     X <- if (!is.empty.model(mt))  #>         model.matrix(mt, mf, contrasts) #>     else matrix(, NROW(Y), 0L) #>     weights <- as.vector(model.weights(mf)) #>     if (!is.null(weights) && !is.numeric(weights))  #>         stop(\"'weights' must be a numeric vector\") #>     if (!is.null(weights) && any(weights < 0))  #>         stop(\"negative weights not allowed\") #>     offset <- as.vector(model.offset(mf)) #>     if (!is.null(offset)) { #>         if (length(offset) != NROW(Y))  #>             stop(gettextf(\"number of offsets is %d should equal %d (number of observations)\",  #>                 length(offset), NROW(Y)), domain = NA) #>     } #>     mustart <- model.extract(mf, \"mustart\") #>     etastart <- model.extract(mf, \"etastart\") #>     fit <- eval(call(if (is.function(method)) \"method\" else method,  #>         x = X, y = Y, weights = weights, start = start, etastart = etastart,  #>         mustart = mustart, offset = offset, family = family,  #>         control = control, intercept = attr(mt, \"intercept\") >  #>             0L, singular.ok = singular.ok)) #>     if (length(offset) && attr(mt, \"intercept\") > 0L) { #>         fit2 <- eval(call(if (is.function(method)) \"method\" else method,  #>             x = X[, \"(Intercept)\", drop = FALSE], y = Y, mustart = fit$fitted.values,  #>             weights = weights, offset = offset, family = family,  #>             control = control, intercept = TRUE)) #>         if (!fit2$converged)  #>             warning(\"fitting to calculate the null deviance did not converge -- increase 'maxit'?\") #>         fit$null.deviance <- fit2$deviance #>     } #>     if (model)  #>         fit$model <- mf #>     fit$na.action <- attr(mf, \"na.action\") #>     if (x)  #>         fit$x <- X #>     if (!y)  #>         fit$y <- NULL #>     structure(c(fit, list(call = cal, formula = formula, terms = mt,  #>         data = data, offset = offset, control = control, method = method,  #>         contrasts = attr(X, \"contrasts\"), xlevels = .getXlevels(mt,  #>             mf))), class = c(fit$class, c(\"glm\", \"lm\"))) #> })(formula = trt ~ age + marker + stage + grade + response +  #>     death + ttdeath, family = structure(list(family = \"binomial\",  #>     link = \"logit\", linkfun = function (mu)  #>     .Call(C_logit_link, mu), linkinv = function (eta)  #>     .Call(C_logit_linkinv, eta), variance = function (mu)  #>     mu * (1 - mu), dev.resids = function (y, mu, wt)  #>     .Call(C_binomial_dev_resids, y, mu, wt), aic = function (y,  #>         n, mu, wt, dev)  #>     { #>         m <- if (any(n > 1))  #>             n #>         else wt #>         -2 * sum(ifelse(m > 0, (wt/m), 0) * dbinom(round(m *  #>             y), round(m), mu, log = TRUE)) #>     }, mu.eta = function (eta)  #>     .Call(C_logit_mu_eta, eta), initialize = { #>         if (NCOL(y) == 1) { #>             if (is.factor(y))  #>                 y <- y != levels(y)[1L] #>             n <- rep.int(1, nobs) #>             y[weights == 0] <- 0 #>             if (any(y < 0 | y > 1))  #>                 stop(\"y values must be 0 <= y <= 1\") #>             mustart <- (weights * y + 0.5)/(weights + 1) #>             m <- weights * y #>             if (\"binomial\" == \"binomial\" && any(abs(m - round(m)) >  #>                 0.001))  #>                 warning(gettextf(\"non-integer #successes in a %s glm!\",  #>                   \"binomial\"), domain = NA) #>         } #>         else if (NCOL(y) == 2) { #>             if (\"binomial\" == \"binomial\" && any(abs(y - round(y)) >  #>                 0.001))  #>                 warning(gettextf(\"non-integer counts in a %s glm!\",  #>                   \"binomial\"), domain = NA) #>             n <- (y1 <- y[, 1L]) + y[, 2L] #>             y <- y1/n #>             if (any(n0 <- n == 0))  #>                 y[n0] <- 0 #>             weights <- weights * n #>             mustart <- (n * y + 0.5)/(n + 1) #>         } #>         else stop(gettextf(\"for the '%s' family, y must be a vector of 0 and 1's\\nor a 2 column matrix where col 1 is no. successes and col 2 is no. failures\",  #>             \"binomial\"), domain = NA) #>     }, validmu = function (mu)  #>     all(is.finite(mu)) && all(mu > 0 & mu < 1), valideta = function (eta)  #>     TRUE, simulate = function (object, nsim)  #>     { #>         ftd <- fitted(object) #>         n <- length(ftd) #>         ntot <- n * nsim #>         wts <- object$prior.weights #>         if (any(wts%%1 != 0))  #>             stop(\"cannot simulate from non-integer prior.weights\") #>         if (!is.null(m <- object$model)) { #>             y <- model.response(m) #>             if (is.factor(y)) { #>                 yy <- factor(1 + rbinom(ntot, size = 1, prob = ftd),  #>                   labels = levels(y)) #>                 split(yy, rep(seq_len(nsim), each = n)) #>             } #>             else if (is.matrix(y) && ncol(y) == 2) { #>                 yy <- vector(\"list\", nsim) #>                 for (i in seq_len(nsim)) { #>                   Y <- rbinom(n, size = wts, prob = ftd) #>                   YY <- cbind(Y, wts - Y) #>                   colnames(YY) <- colnames(y) #>                   yy[[i]] <- YY #>                 } #>                 yy #>             } #>             else rbinom(ntot, size = wts, prob = ftd)/wts #>         } #>         else rbinom(ntot, size = wts, prob = ftd)/wts #>     }, dispersion = 1), class = \"family\"), data = structure(list( #>     trt = structure(c(1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,  #>     2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,  #>     2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L,  #>     2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L,  #>     1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 2L,  #>     2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L), levels = c(\"Drug A\",  #>     \"Drug B\"), class = \"factor\", label = \"Chemotherapy Treatment\"),  #>     age = structure(c(23, 9, 31, NA, 51, 39, 37, 32, 31, 34,  #>     42, 63, 54, 21, 48, 71, 38, 49, 57, 46, 47, 52, 61, 38, 34,  #>     49, 63, 67, 68, 78, 36, 37, 53, 36, 51, 48, 57, 31, 37, 28,  #>     40, 49, 61, 56, 54, 71, 38, 31, 48, NA, 83, 52, 32, 53, 69,  #>     60, 45, 39, NA, 38, 36, 71, 31, 43, 57, 53, 25, 44, 25, 30,  #>     51, 40, NA, 43, 21, 54, 67, 43, 54, 41, 34, 34, 6, 39, 36,  #>     58, 27, 47, NA, 50, 61, 47, 52, 51, 68, 33, 65, 34, 38, 60,  #>     10, 49, 56, 50, 60, 49, 54, 39, 48, 65, 47, 61, 34, NA, NA,  #>     58, 26, 44, 17, 68, 57, 66, 44, NA, 67, 48, 62, 35, 53, 53,  #>     66, 55, 57, 47, 58, 43, 45, 44, 63, 59, 44, 53, 51, 28, 65,  #>     63, 76, 61, 33, 48, 42, 36, 55, 20, 26, 50, 47, 74, 50, 31,  #>     45, 51, 66, 76, 47, 48, 56, 70, 46, 43, 41, 41, 19, 49, 43,  #>     43, 75, 52, 42, 37, 45, 35, 67, 38, 44, 45, 39, 46, NA, 42,  #>     60, 31, 45, 38, NA, 19, 69, 66, NA, 64), label = \"Age\"),  #>     marker = structure(c(0.16, 1.107, 0.277, 2.067, 2.767, 0.613,  #>     0.354, 1.739, 0.144, 0.205, 0.513, 0.06, 0.831, 0.258, 0.128,  #>     0.445, 2.083, 0.157, 0.066, 0.325, 0.266, 0.719, 1.713, 0.096,  #>     0.105, 0.043, 0.981, 1.156, 0.105, 0.175, 0.309, 1.869, 2.008,  #>     1.894, 0.16, 1.209, 0.108, 0.611, 0.222, 0.803, 0.37, NA,  #>     0.177, 1.479, 0.161, 0.737, 0.124, 0.092, 0.385, 0.21, 0.475,  #>     1.628, 0.583, NA, 0.702, 1.206, 2.213, 1.406, 0.101, 0.013,  #>     2.032, 1.046, 0.408, 2.636, 1.263, NA, 2.447, 1.041, 0.531,  #>     0.924, 1.087, 0.733, 2.157, 0.333, 1.527, 2.238, 0.153, 0.305,  #>     0.131, 0.386, 1.645, 1.321, 0.229, 0.615, 1.976, 1.941, 0.22,  #>     3.874, 0.982, 1.68, 1.091, 0.169, 0.511, 2.141, 0.599, NA,  #>     0.389, 0.005, 0.075, 1.491, 0.358, 1.709, 0.056, 1.354, 2.522,  #>     0.387, 0.592, 0.243, 0.215, 1.207, 0.29, 0.718, 0.589, 0.003,  #>     1.328, 0.308, 0.691, 3.249, 0.039, 1.804, 0.238, 2.702, 1.441,  #>     0.27, NA, NA, 0.062, 2.19, 0.976, 3.062, 0.124, 0.045, 1.892,  #>     0.711, 1.079, 1.061, 0.239, 0.361, 0.033, 1.133, 1.225, 1.418,  #>     3.751, 3.02, 0.086, 0.772, 1.882, 2.725, 2.41, 0.352, 0.895,  #>     0.215, 0.141, 2.288, 1.658, 1.255, 1.306, 0.081, 0.667, 0.046,  #>     0.662, 1.985, 1.063, 1.55, 0.015, 0.056, NA, 0.51, 0.929,  #>     2.345, 0.25, 0.816, 0.022, 0.16, 0.547, 3.642, 0.092, 1.2,  #>     1.512, 2.124, NA, 0.862, 0.182, 1.075, 0.021, 0.402, 0.063,  #>     1.129, 0.61, NA, 0.717, 0.205, 0.946, 0.386, 0.37, 1.148,  #>     NA, 0.136, 0.439, 1.148), label = \"Marker Level (ng/mL)\"),  #>     stage = structure(c(1L, 2L, 1L, 3L, 4L, 4L, 1L, 1L, 1L, 3L,  #>     1L, 3L, 4L, 4L, 1L, 4L, 4L, 2L, 1L, 1L, 2L, 2L, 4L, 4L, 4L,  #>     2L, 4L, 1L, 4L, 3L, 1L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 4L, 4L,  #>     3L, 1L, 4L, 3L, 4L, 1L, 1L, 2L, 1L, 4L, 1L, 2L, 2L, 3L, 3L,  #>     2L, 4L, 1L, 4L, 2L, 4L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 4L, 1L,  #>     2L, 2L, 2L, 1L, 4L, 4L, 2L, 2L, 4L, 4L, 3L, 2L, 4L, 3L, 2L,  #>     4L, 1L, 2L, 1L, 4L, 3L, 3L, 1L, 3L, 2L, 3L, 2L, 2L, 3L, 4L,  #>     4L, 3L, 3L, 2L, 3L, 2L, 2L, 3L, 2L, 1L, 1L, 3L, 4L, 1L, 4L,  #>     3L, 3L, 2L, 4L, 2L, 1L, 2L, 1L, 4L, 3L, 3L, 3L, 2L, 1L, 2L,  #>     1L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 3L, 4L, 1L, 2L, 2L,  #>     1L, 3L, 4L, 2L, 4L, 2L, 1L, 2L, 3L, 1L, 3L, 4L, 2L, 2L, 1L,  #>     2L, 2L, 3L, 1L, 2L, 2L, 1L, 1L, 3L, 2L, 3L, 1L, 1L, 2L, 4L,  #>     2L, 4L, 4L, 2L, 3L, 4L, 3L, 4L, 4L, 1L, 1L, 4L, 4L, 4L, 1L,  #>     2L, 2L, 2L, 4L, 3L, 3L, 2L, 2L, 4L, 3L), levels = c(\"T1\",  #>     \"T2\", \"T3\", \"T4\"), class = \"factor\", label = \"T Stage\"),  #>     grade = structure(c(2L, 1L, 2L, 3L, 3L, 1L, 2L, 1L, 2L, 1L,  #>     3L, 1L, 3L, 1L, 1L, 3L, 3L, 2L, 3L, 2L, 1L, 2L, 1L, 1L, 2L,  #>     3L, 2L, 2L, 2L, 1L, 3L, 2L, 1L, 1L, 1L, 3L, 2L, 2L, 3L, 2L,  #>     2L, 3L, 3L, 1L, 3L, 1L, 3L, 2L, 2L, 2L, 3L, 3L, 3L, 2L, 3L,  #>     1L, 3L, 1L, 2L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 3L, 2L,  #>     1L, 3L, 3L, 3L, 2L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L,  #>     3L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 3L, 1L,  #>     3L, 1L, 2L, 2L, 1L, 2L, 2L, 3L, 1L, 3L, 3L, 1L, 1L, 1L, 2L,  #>     3L, 3L, 2L, 1L, 3L, 2L, 1L, 2L, 2L, 2L, 1L, 3L, 3L, 2L, 3L,  #>     1L, 1L, 1L, 2L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L,  #>     2L, 2L, 2L, 2L, 1L, 1L, 3L, 2L, 2L, 1L, 2L, 1L, 2L, 3L, 2L,  #>     1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L,  #>     3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L,  #>     3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c(\"I\",  #>     \"II\", \"III\"), class = \"factor\", label = \"Grade\"), response = structure(c(1L,  #>     2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L,  #>     2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L,  #>     1L, 1L, 2L, 1L, NA, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L,  #>     2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L,  #>     1L, 1L, 1L, NA, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L,  #>     1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L, 1L, 2L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,  #>     1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L,  #>     2L, 2L, NA, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, NA, 2L, 1L,  #>     1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L,  #>     1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, NA, 1L, 2L,  #>     1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L,  #>     2L, 2L, 1L, 1L), levels = c(\"0\", \"1\"), class = \"factor\", label = \"Tumor Response\"),  #>     death = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L,  #>     1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L,  #>     2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,  #>     2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L,  #>     2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L,  #>     1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L,  #>     2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L,  #>     2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L,  #>     1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L,  #>     1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,  #>     1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L,  #>     1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L,  #>     1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L,  #>     1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L), levels = c(\"0\",  #>     \"1\"), class = \"factor\", label = \"Patient Died\"), ttdeath = structure(c(24,  #>     24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24,  #>     14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92,  #>     23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24,  #>     24, 21.19, 12.52, 24, 15.59, 18, 18.02, 12.43, 12.1, 24,  #>     17.42, 24, 24, 24, 12.19, 10.02, 18.23, 10.42, 24, 24, 19.34,  #>     12.21, 14.46, 19.34, 10.16, 13.15, 10.12, 24, 22.77, 24,  #>     24, 22.13, 24, 20.62, 23.23, 7.38, 24, 24, 24, 24, 24, 19.22,  #>     7.27, 23.88, 16.23, 24, 14.06, 24, 24, 24, 16.44, 23.81,  #>     24, 18.37, 11.44, 20.94, 5.33, 22.92, 10.33, 24, 24, 14.54,  #>     19.14, 24, 21.19, 16.07, 9.97, 24, 24, 24, 19.75, 16.67,  #>     11.18, 18.29, 24, 17.56, 17.45, 24, 22.86, 13.68, 24, 24,  #>     17.46, 24, 24, 24, 24, 24, 13, 9.73, 15.65, 24, 3.53, 20.35,  #>     23.41, 16.47, 24, 24, 14.65, 17.81, 24, 21.83, 24, 24, 21.49,  #>     12.68, 24, 24, 24, 24, 10.07, 24, 24, 24, 8.37, 20.33, 24,  #>     24, 21.33, 12.63, 13.08, 24, 15.1, 20.14, 10.55, 24, 24,  #>     24, 24, 23.6, 24, 19.98, 15.55, 23.72, 22.41, 19.54, 16.57,  #>     24, 24, 24, 21.91, 24, 12.53, 24, 18.63, 14.82, 16.46, 24,  #>     9.24, 17.77, 24, 24, 9.92, 16.16, 10.51, 20.81, 24, 16.44,  #>     24, 22.4, 11.76, 24, 21.6, 24, 19.81, 24), label = \"Months to Death/Censor\")), class = c(\"tbl_df\",  #> \"tbl\", \"data.frame\"), row.names = c(NA, -200L))) #>  #> Coefficients: #> (Intercept)          age       marker      stageT2      stageT3      stageT4   #>    1.652845    -0.002014    -0.259849     0.404341     0.117402    -0.002102   #>     gradeII     gradeIII    response1       death1      ttdeath   #>   -0.037012     0.022890     0.498952    -0.003916    -0.076073   #>  #> Degrees of Freedom: 172 Total (i.e. Null);  162 Residual #>   (27 observations deleted due to missingness) #> Null Deviance:\t    239.5  #> Residual Deviance: 230.9 \tAIC: 252.9 m <- mtcars |>   default_parsing() |>   regression_model(     outcome.str = \"mpg\",     auto.mode = FALSE,     fun = \"stats::lm\",     formula.str = \"{outcome.str}~{paste(vars,collapse='+')}\",     args.list = NULL,     vars = c(\"mpg\", \"cyl\")   )   broom::tidy(m) #> # A tibble: 3 × 5 #>   term        estimate std.error statistic  p.value #>   <chr>          <dbl>     <dbl>     <dbl>    <dbl> #> 1 (Intercept)    26.7      0.972     27.4  2.69e-22 #> 2 cyl6           -6.92     1.56      -4.44 1.19e- 4 #> 3 cyl8          -11.6      1.30      -8.90 8.57e-10 if (FALSE) { # \\dontrun{ gtsummary::trial |>   regression_model_uv(outcome.str = \"age\") gtsummary::trial |>   regression_model_uv(     outcome.str = \"age\",     fun = \"stats::lm\",     args.list = NULL   ) m <- gtsummary::trial |> regression_model_uv(   outcome.str = \"trt\",   fun = \"stats::glm\",   args.list = list(family = stats::binomial(link = \"logit\")) ) lapply(m,broom::tidy) |> dplyr::bind_rows() } # } if (FALSE) { # \\dontrun{ gtsummary::trial |>   regression_model(     outcome.str = \"age\",     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) ls <- regression_model_list(data = default_parsing(mtcars), outcome.str = \"cyl\", fun.descr = \"Ordinal logistic regression model\") summary(ls$model)  ls <- regression_model_list(data = default_parsing(gtsummary::trial), outcome.str = \"trt\", fun.descr = \"Logistic regression model\") tbl <- gtsummary::tbl_regression(ls$model, exponentiate = TRUE) m <- gtsummary::trial |>   default_parsing() |>   regression_model(     outcome.str = \"trt\",     fun = \"stats::glm\",     formula.str = \"{outcome.str}~.\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) tbl2 <- gtsummary::tbl_regression(m, exponentiate = TRUE) broom::tidy(ls$model) broom::tidy(m) } # } if (FALSE) { # \\dontrun{ gtsummary::trial |> regression_model_uv(   outcome.str = \"trt\",   fun = \"stats::glm\",   args.list = list(family = stats::binomial(link = \"logit\")) ) |> lapply(broom::tidy) |> dplyr::bind_rows() ms <- regression_model_uv_list(data = default_parsing(mtcars), outcome.str = \"mpg\", fun.descr = \"Linear regression model\") lapply(ms$model,broom::tidy) |> dplyr::bind_rows() } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":null,"dir":"Reference","previous_headings":"","what":"Create table of regression model — regression_table","title":"Create table of regression model — regression_table","text":"Create table regression model","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create table of regression model — regression_table","text":"","code":"regression_table(x, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create table of regression model — regression_table","text":"x regression model ... passed methods args.list list arguments passed 'fun'. fun function use table creation. Default \"gtsummary::tbl_regression\".","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create table of regression model — regression_table","text":"object standard class fun","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/regression_table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create table of regression model — regression_table","text":"","code":"if (FALSE) { # \\dontrun{ tbl <- gtsummary::trial |>   regression_model(     outcome.str = \"stage\",     fun = \"MASS::polr\"   ) |>   regression_table(args.list = list(\"exponentiate\" = TRUE)) gtsummary::trial |>   regression_model(     outcome.str = \"age\",     fun = \"stats::lm\",     formula.str = \"{outcome.str}~.\",     args.list = NULL   ) |>   regression_table() |> plot() gtsummary::trial |>   regression_model(     outcome.str = \"trt\",     fun = \"stats::glm\",     args.list = list(family = binomial(link = \"logit\"))   ) |>   regression_table() gtsummary::trial |>   regression_model_uv(     outcome.str = \"trt\",     fun = \"stats::glm\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) |>   regression_table() gtsummary::trial |>   regression_model_uv(     outcome.str = \"stage\",     args.list = list(family = stats::binomial(link = \"logit\"))   ) |>   regression_table()  list(   \"Univariable\" = regression_model_uv,   \"Multivariable\" = regression_model ) |>   lapply(\\(.fun){     do.call(       .fun,       c(         list(data = gtsummary::trial),         list(outcome.str = \"stage\")       )     )   }) |>   purrr::map(regression_table) |>   tbl_merge()   } # } regression_table <- function(x, ...) {   UseMethod(\"regression_table\") }  #' @rdname regression_table #' @export regression_table.list <- function(x, ...) {   x |>     purrr::map(\\(.m){       regression_table(x = .m, ...) |>         gtsummary::add_n()     }) |>     gtsummary::tbl_stack() }  #' @rdname regression_table #' @export regression_table.default <- function(x, ..., args.list = NULL, fun = \"gtsummary::tbl_regression\") {   # Stripping custom class   class(x) <- class(x)[class(x) != \"freesearcher_model\"]    if (any(c(length(class(x)) != 1, class(x) != \"lm\"))) {     if (!\"exponentiate\" %in% names(args.list)) {       args.list <- c(args.list, list(exponentiate = TRUE))     }   }    out <- do.call(getfun(fun), c(list(x = x), args.list))   out |>     gtsummary::add_glance_source_note() # |>   # gtsummary::bold_p() }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Removes columns with completenes below cutoff — remove_empty_cols","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"Removes columns completenes cutoff","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"","code":"remove_empty_cols(data, cutoff = 0.7)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"data data frame cutoff numeric","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"data frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_empty_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Removes columns with completenes below cutoff — remove_empty_cols","text":"","code":"data.frame(a=1:10,b=NA, c=c(2,NA)) |> remove_empty_cols(cutoff=.5) #>     a  c #> 1   1  2 #> 2   2 NA #> 3   3  2 #> 4   4 NA #> 5   5  2 #> 6   6 NA #> 7   7  2 #> 8   8 NA #> 9   9  2 #> 10 10 NA"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove NA labels — remove_na_attr","title":"Remove NA labels — remove_na_attr","text":"Remove NA labels","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove NA labels — remove_na_attr","text":"","code":"remove_na_attr(data, attr = \"label\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove NA labels — remove_na_attr","text":"data data","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove NA labels — remove_na_attr","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/remove_na_attr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove NA labels — remove_na_attr","text":"","code":"ds <- mtcars |> lapply(\\(.x) REDCapCAST::set_attr(.x,label=NA,attr = \"label\")) ds |> remove_na_attr() |> str() #> tibble [32 × 11] (S3: tbl_df/tbl/data.frame) #>  $ mpg : num [1:32] 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #>  $ cyl : num [1:32] 6 6 4 6 8 6 8 4 4 6 ... #>  $ disp: num [1:32] 160 160 108 258 360 ... #>  $ hp  : num [1:32] 110 110 93 110 175 105 245 62 95 123 ... #>  $ drat: num [1:32] 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #>  $ wt  : num [1:32] 2.62 2.88 2.32 3.21 3.44 ... #>  $ qsec: num [1:32] 16.5 17 18.6 19.4 17 ... #>  $ vs  : num [1:32] 0 0 1 1 0 1 0 1 1 1 ... #>  $ am  : num [1:32] 1 1 1 0 0 0 0 0 0 0 ... #>  $ gear: num [1:32] 4 4 4 3 3 3 3 4 4 4 ... #>  $ carb: num [1:32] 4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/freesearcheR/reference/sankey_ready.html","id":null,"dir":"Reference","previous_headings":"","what":"Readying data for sankey plot — sankey_ready","title":"Readying data for sankey plot — sankey_ready","text":"Readying data sankey plot","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/sankey_ready.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Readying data for sankey plot — sankey_ready","text":"","code":"sankey_ready(data, x, y, z = NULL, numbers = \"count\")"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/sankey_ready.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Readying data for sankey plot — sankey_ready","text":"z","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/sankey_ready.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Readying data for sankey plot — sankey_ready","text":"","code":"ds <- data.frame(g = sample(LETTERS[1:2], 100, TRUE), first = REDCapCAST::as_factor(sample(letters[1:4], 100, TRUE)), last = sample(c(letters[1:4], NA), 100, TRUE, prob = c(rep(.23, 4), .08))) ds |> sankey_ready(\"first\", \"last\") #> # A tibble: 20 × 7 #>    first last      n gx.sum gy.sum lx          ly          #>    <fct> <chr> <int>  <int>  <int> <fct>       <fct>       #>  1 d     a         5     22     17 \"d\\n(n=22)\" \"a\\n(n=17)\" #>  2 d     b         8     22     25 \"d\\n(n=22)\" \"b\\n(n=25)\" #>  3 d     c         4     22     29 \"d\\n(n=22)\" \"c\\n(n=29)\" #>  4 d     d         4     22     22 \"d\\n(n=22)\" \"d\\n(n=22)\" #>  5 d     NA        1     22      7 \"d\\n(n=22)\" \"NA\\n(n=7)\" #>  6 b     a         1     32     17 \"b\\n(n=32)\" \"a\\n(n=17)\" #>  7 b     b        11     32     25 \"b\\n(n=32)\" \"b\\n(n=25)\" #>  8 b     c        12     32     29 \"b\\n(n=32)\" \"c\\n(n=29)\" #>  9 b     d         7     32     22 \"b\\n(n=32)\" \"d\\n(n=22)\" #> 10 b     NA        1     32      7 \"b\\n(n=32)\" \"NA\\n(n=7)\" #> 11 a     a         8     23     17 \"a\\n(n=23)\" \"a\\n(n=17)\" #> 12 a     b         2     23     25 \"a\\n(n=23)\" \"b\\n(n=25)\" #> 13 a     c         7     23     29 \"a\\n(n=23)\" \"c\\n(n=29)\" #> 14 a     d         4     23     22 \"a\\n(n=23)\" \"d\\n(n=22)\" #> 15 a     NA        2     23      7 \"a\\n(n=23)\" \"NA\\n(n=7)\" #> 16 c     a         3     23     17 \"c\\n(n=23)\" \"a\\n(n=17)\" #> 17 c     b         4     23     25 \"c\\n(n=23)\" \"b\\n(n=25)\" #> 18 c     c         6     23     29 \"c\\n(n=23)\" \"c\\n(n=29)\" #> 19 c     d         7     23     22 \"c\\n(n=23)\" \"d\\n(n=22)\" #> 20 c     NA        3     23      7 \"c\\n(n=23)\" \"NA\\n(n=7)\" ds |> sankey_ready(\"first\", \"last\", numbers = \"percentage\") #> # A tibble: 20 × 7 #>    first last      n gx.sum gy.sum lx         ly         #>    <fct> <chr> <int>  <int>  <int> <fct>      <fct>      #>  1 d     a         5     22     17 \"d\\n(22%)\" \"a\\n(17%)\" #>  2 d     b         8     22     25 \"d\\n(22%)\" \"b\\n(25%)\" #>  3 d     c         4     22     29 \"d\\n(22%)\" \"c\\n(29%)\" #>  4 d     d         4     22     22 \"d\\n(22%)\" \"d\\n(22%)\" #>  5 d     NA        1     22      7 \"d\\n(22%)\" \"NA\\n(7%)\" #>  6 b     a         1     32     17 \"b\\n(32%)\" \"a\\n(17%)\" #>  7 b     b        11     32     25 \"b\\n(32%)\" \"b\\n(25%)\" #>  8 b     c        12     32     29 \"b\\n(32%)\" \"c\\n(29%)\" #>  9 b     d         7     32     22 \"b\\n(32%)\" \"d\\n(22%)\" #> 10 b     NA        1     32      7 \"b\\n(32%)\" \"NA\\n(7%)\" #> 11 a     a         8     23     17 \"a\\n(23%)\" \"a\\n(17%)\" #> 12 a     b         2     23     25 \"a\\n(23%)\" \"b\\n(25%)\" #> 13 a     c         7     23     29 \"a\\n(23%)\" \"c\\n(29%)\" #> 14 a     d         4     23     22 \"a\\n(23%)\" \"d\\n(22%)\" #> 15 a     NA        2     23      7 \"a\\n(23%)\" \"NA\\n(7%)\" #> 16 c     a         3     23     17 \"c\\n(23%)\" \"a\\n(17%)\" #> 17 c     b         4     23     25 \"c\\n(23%)\" \"b\\n(25%)\" #> 18 c     c         6     23     29 \"c\\n(23%)\" \"c\\n(29%)\" #> 19 c     d         7     23     22 \"c\\n(23%)\" \"d\\n(22%)\" #> 20 c     NA        3     23      7 \"c\\n(23%)\" \"NA\\n(7%)\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the freesearcheR tool locally — shiny_freesearcheR","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"data.frames global environment accessible app.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"","code":"shiny_freesearcheR(...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"... arguments passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/shiny_freesearcheR.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Launch the freesearcheR tool locally — shiny_freesearcheR","text":"","code":"if (FALSE) { # \\dontrun{ data(mtcars) shiny_freesearcheR(launch.browser = TRUE) } # }"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"Specify format arguments include qmd header/frontmatter","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"","code":"specify_qmd_format(data, fileformat = c(\"docx\", \"odt\", \"pdf\", \"all\"))"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"data vector fileformat format include","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/specify_qmd_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specify format arguments to include in qmd header/frontmatter — specify_qmd_format","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":null,"dir":"Reference","previous_headings":"","what":"Easily subset by data type function — subset_types","title":"Easily subset by data type function — subset_types","text":"Easily subset data type function","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Easily subset by data type function — subset_types","text":"","code":"subset_types(data, types, type.fun = outcome_type)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Easily subset by data type function — subset_types","text":"data data types desired types type.fun function get type. Default outcome_type","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Easily subset by data type function — subset_types","text":"vector","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/subset_types.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Easily subset by data type function — subset_types","text":"","code":"default_parsing(mtcars) |> subset_types(\"ordinal\") #> # A tibble: 32 × 3 #>    cyl   gear  carb  #>    <fct> <fct> <fct> #>  1 6     4     4     #>  2 6     4     4     #>  3 4     4     1     #>  4 6     3     1     #>  5 8     3     2     #>  6 6     3     1     #>  7 8     3     4     #>  8 4     4     2     #>  9 4     4     2     #> 10 6     4     4     #> # ℹ 22 more rows default_parsing(mtcars) |> subset_types(c(\"dichotomous\", \"ordinal\")) #> # A tibble: 32 × 5 #>    cyl   vs    am    gear  carb  #>    <fct> <fct> <fct> <fct> <fct> #>  1 6     0     1     4     4     #>  2 6     0     1     4     4     #>  3 4     1     1     4     1     #>  4 6     1     0     3     1     #>  5 8     0     0     3     2     #>  6 6     1     0     3     1     #>  7 8     0     0     3     4     #>  8 4     1     0     4     2     #>  9 4     1     0     4     2     #> 10 6     1     0     4     4     #> # ℹ 22 more rows #' default_parsing(mtcars) |> subset_types(\"factor\",class)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Implemented functions — supported_functions","title":"Implemented functions — supported_functions","text":"Library supported functions. list name \"descr\" element unique element list.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Implemented functions — supported_functions","text":"","code":"supported_functions()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Implemented functions — supported_functions","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_functions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Implemented functions — supported_functions","text":"","code":"supported_functions() #> $lm #> $lm$descr #> [1] \"Linear regression model\" #>  #> $lm$design #> [1] \"cross-sectional\" #>  #> $lm$out.type #> [1] \"continuous\" #>  #> $lm$fun #> [1] \"stats::lm\" #>  #> $lm$args.list #> NULL #>  #> $lm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $lm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $lm$table.args.list #> $lm$table.args.list$exponentiate #> [1] FALSE #>  #>  #>  #> $glm #> $glm$descr #> [1] \"Logistic regression model\" #>  #> $glm$design #> [1] \"cross-sectional\" #>  #> $glm$out.type #> [1] \"dichotomous\" #>  #> $glm$fun #> [1] \"stats::glm\" #>  #> $glm$args.list #> $glm$args.list$family #>  #> Family: binomial  #> Link function: logit  #>  #>  #>  #> $glm$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $glm$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $glm$table.args.list #> list() #>  #>  #> $polr #> $polr$descr #> [1] \"Ordinal logistic regression model\" #>  #> $polr$design #> [1] \"cross-sectional\" #>  #> $polr$out.type #> [1] \"ordinal\" #>  #> $polr$fun #> [1] \"MASS::polr\" #>  #> $polr$args.list #> $polr$args.list$Hess #> [1] TRUE #>  #> $polr$args.list$method #> [1] \"logistic\" #>  #>  #> $polr$formula.str #> [1] \"{outcome.str}~{paste(vars,collapse='+')}\" #>  #> $polr$table.fun #> [1] \"gtsummary::tbl_regression\" #>  #> $polr$table.args.list #> list() #>  #>"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":null,"dir":"Reference","previous_headings":"","what":"Implemented functions — supported_plots","title":"Implemented functions — supported_plots","text":"Library supported functions. list name \"descr\" element unique element list. descr: Plot description primary.type: Primary variable data type (continuous, dichotomous ordinal) secondary.type: Secondary variable data type (continuous, dichotomous ordinal) secondary.extra: \"none\" NULL option choose none. tertiary.type: Tertiary variable data type (continuous, dichotomous ordinal)","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Implemented functions — supported_plots","text":"","code":"supported_plots()"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Implemented functions — supported_plots","text":"list","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/supported_plots.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Implemented functions — supported_plots","text":"","code":"supported_plots() |> str() #> List of 5 #>  $ plot_hbars  :List of 6 #>   ..$ descr          : chr \"Stacked horizontal bars\" #>   ..$ note           : chr \"A classical way of visualising the distribution of an ordinal scale like the modified Ranking Scale and known as Grotta bars\" #>   ..$ primary.type   : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: chr \"none\" #>  $ plot_violin :List of 6 #>   ..$ descr          : chr \"Violin plot\" #>   ..$ note           : chr \"A modern alternative to the classic boxplot to visualise data distribution\" #>   ..$ primary.type   : chr [1:3] \"continuous\" \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: chr \"none\" #>  $ plot_ridge  :List of 6 #>   ..$ descr          : chr \"Ridge plot\" #>   ..$ note           : chr \"An alternative option to visualise data distribution\" #>   ..$ primary.type   : chr \"continuous\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: NULL #>  $ plot_sankey :List of 6 #>   ..$ descr          : chr \"Sankey plot\" #>   ..$ note           : chr \"A way of visualising change between groups\" #>   ..$ primary.type   : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.type : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: NULL #>  $ plot_scatter:List of 6 #>   ..$ descr          : chr \"Scatter plot\" #>   ..$ note           : chr \"A classic way of showing the association between to variables\" #>   ..$ primary.type   : chr \"continuous\" #>   ..$ secondary.type : chr [1:2] \"continuous\" \"ordinal\" #>   ..$ tertiary.type  : chr [1:2] \"dichotomous\" \"ordinal\" #>   ..$ secondary.extra: NULL"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":null,"dir":"Reference","previous_headings":"","what":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"substitue gtsummary::tbl_merge, use list names tab spanner names.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"","code":"tbl_merge(data)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"data gtsummary list object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/tbl_merge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A substitue to gtsummary::tbl_merge, that will use list names for the tab spanner names. — tbl_merge","text":"gt summary list object","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Module to Reorder the Levels of a Factor Variable — update-factor","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"module contain interface reorder levels factor variable.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"","code":"update_factor_ui(id)  update_factor_server(id, data_r = reactive(NULL))  modal_update_factor(   id,   title = i18n(\"Update levels of a factor\"),   easyClose = TRUE,   size = \"l\",   footer = NULL )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"id Module ID. data_r shiny::reactive() function returning data.frame. title optional title dialog. easyClose TRUE, modal dialog can dismissed clicking outside dialog box, pressing Escape key. FALSE (default), modal dialog dismissed ways; instead must dismissed clicking modalButton(), call removeModal() server. size One \"s\" small, \"m\" (default) medium, \"l\" large, \"xl\" extra large. Note \"xl\" works Bootstrap 4 (opt-Bootstrap 4+, pass bslib::bs_theme() theme argument page container like fluidPage()). footer UI footer. Use NULL footer.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-factor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module to Reorder the Levels of a Factor Variable — update-factor","text":"shiny::reactive() function returning data.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Select, rename and convert variables — update-variables","title":"Select, rename and convert variables — update-variables","text":"Select, rename convert variables","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select, rename and convert variables — update-variables","text":"","code":"update_variables_ui(id, title = TRUE)  update_variables_server(   id,   data,   height = NULL,   return_data_on_init = FALSE,   try_silent = FALSE )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select, rename and convert variables — update-variables","text":"id Module's ID title Module's title, TRUE use default title, use NULL title shiny.tag custom one. data data.frame reactive function returning data.frame. height Height table. return_data_on_init Return initial data module called. try_silent logical: report error messages suppressed?","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update-variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select, rename and convert variables — update-variables","text":"shiny::reactive() function returning updated data.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Modified from the datamods pacakge — update_variables_datagrid","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"Modified datamods pacakge","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"","code":"update_variables_datagrid(   data,   height = NULL,   selectionId = NULL,   buttonId = NULL )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"data data height height selectionId selectionId buttonId buttonId","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/update_variables_datagrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modified from the datamods pacakge — update_variables_datagrid","text":"","code":"mtcars |>   summary_vars() |>   update_variables_datagrid() #> Error in update_variables_datagrid(summary_vars(mtcars)): could not find function \"update_variables_datagrid\""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":null,"dir":"Reference","previous_headings":"","what":"Vertical stacked bar plot wrapper — vertical_stacked_bars","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"Vertical stacked bar plot wrapper","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"","code":"vertical_stacked_bars(   data,   score = \"full_score\",   group = \"pase_0_q\",   strata = NULL,   t.size = 10,   l.color = \"black\",   l.size = 0.5,   draw.lines = TRUE )"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/vertical_stacked_bars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vertical stacked bar plot wrapper — vertical_stacked_bars","text":"t.size","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"Wrapper save data RDS, load specified qmd render","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"","code":"write_quarto(data, ...)"},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"data list pass qmd ... Passed quarto::quarto_render()","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/reference/write_quarto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrapper to save data in RDS, load into specified qmd and render — write_quarto","text":"output file name","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-2531","dir":"Changelog","previous_headings":"","what":"freesearcheR 25.3.1","title":"freesearcheR 25.3.1","text":"First steps towards focused simplified interface. Focus ease use, handling basic functionality data inspection descriptive analyses. Inspired Stroke Center implementation guidelines WSO, apply similar approach project order keep interface simple robust. Basic functions descriptive analyses data browsing basics. advanced features like regression analyses added learning purposes, really done one self software like R ensure learning reproducibility. Teal dependencies removed. teal framework really seems powerful promising, also mean less control clutter. May come later. main components implemented: Data import different sources Data management (variable creation, re-classing, naming, labelling ) Basic data comparisons descriptive analyses Basic data visualisations select set plot types great publication purposes Regression analysis basic clinical cross-sectional data (mixed models repeated measures survival analyses table) Export outputs (descriptive analyses regression) well modified dataset (code also showed, working ) Next steps : Polished code export Improved workflow descriptive text well thorough step-wise guide/documentation (possibly small videos) Implement clinical projects Implement data analysis courses Extensive testing bug squashing","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-2511","dir":"Changelog","previous_headings":"","what":"freesearcheR 25.1.1","title":"freesearcheR 25.1.1","text":"UI tweaks. NEW: Option set class hms using hms package. NEW: summary grid sparklines. Speed improvements better regression analysis handling. Preparations extending analysis options study designs.","code":""},{"path":"https://agdamsbo.github.io/freesearcheR/news/index.html","id":"freesearcher-24121","dir":"Changelog","previous_headings":"","what":"freesearcheR 24.12.1","title":"freesearcheR 24.12.1","text":"Initial release Zenodo.","code":""}]