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agdamsbo 2025-05-13 06:33:41 +00:00
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commit 8503118101
4 changed files with 4 additions and 89 deletions
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2
pkgdown.yml
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@ -6,7 +6,7 @@ articles:
FreesearchR: FreesearchR.html FreesearchR: FreesearchR.html
session: session.html session: session.html
visuals: visuals.html visuals: visuals.html
last_built: 2025-05-12T12:15Z last_built: 2025-05-13T06:32Z
urls: urls:
reference: https://agdamsbo.github.io/FreesearchR/reference reference: https://agdamsbo.github.io/FreesearchR/reference
article: https://agdamsbo.github.io/FreesearchR/articles article: https://agdamsbo.github.io/FreesearchR/articles

2
reference/getfun.html
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@ -138,7 +138,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> z$qr &lt;- NULL</span> <span class="r-out co"><span class="r-pr">#&gt;</span> z$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> 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> }</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x55771ca00460&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;bytecode: 0x55fda49cbf60&gt;</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: namespace:stats&gt;</span> <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: namespace:stats&gt;</span>
</code></pre></div> </code></pre></div>
</div> </div>

87
reference/regression_table.html
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@ -77,92 +77,7 @@
<div class="section level2"> <div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span> <span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="va">tbl</span> <span class="op">&lt;-</span> <span class="fu">gtsummary</span><span class="fu">::</span><span class="va"><a href="https://www.danieldsjoberg.com/gtsummary/reference/trial.html" class="external-link">trial</a></span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="regression_model.html">regression_model</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> outcome.str <span class="op">=</span> <span class="st">"stage"</span>,</span></span>
<span class="r-in"><span> fun <span class="op">=</span> <span class="st">"MASS::polr"</span></span></span>
<span class="r-in"><span> <span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">regression_table</span><span class="op">(</span>args.list <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"exponentiate"</span> <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">gtsummary</span><span class="fu">::</span><span class="va"><a href="https://www.danieldsjoberg.com/gtsummary/reference/trial.html" class="external-link">trial</a></span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="regression_model.html">regression_model</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> outcome.str <span class="op">=</span> <span class="st">"age"</span>,</span></span>
<span class="r-in"><span> fun <span class="op">=</span> <span class="st">"stats::lm"</span>,</span></span>
<span class="r-in"><span> formula.str <span class="op">=</span> <span class="st">"{outcome.str}~."</span>,</span></span>
<span class="r-in"><span> args.list <span class="op">=</span> <span class="cn">NULL</span></span></span>
<span class="r-in"><span> <span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">regression_table</span><span class="op">(</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">gtsummary</span><span class="fu">::</span><span class="va"><a href="https://www.danieldsjoberg.com/gtsummary/reference/trial.html" class="external-link">trial</a></span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="regression_model.html">regression_model</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> outcome.str <span class="op">=</span> <span class="st">"trt"</span>,</span></span>
<span class="r-in"><span> fun <span class="op">=</span> <span class="st">"stats::glm"</span>,</span></span>
<span class="r-in"><span> args.list <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>family <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/family.html" class="external-link">binomial</a></span><span class="op">(</span>link <span class="op">=</span> <span class="st">"logit"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">regression_table</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">gtsummary</span><span class="fu">::</span><span class="va"><a href="https://www.danieldsjoberg.com/gtsummary/reference/trial.html" class="external-link">trial</a></span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="regression_model.html">regression_model_uv</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> outcome.str <span class="op">=</span> <span class="st">"trt"</span>,</span></span>
<span class="r-in"><span> fun <span class="op">=</span> <span class="st">"stats::glm"</span>,</span></span>
<span class="r-in"><span> args.list <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>family <span class="op">=</span> <span class="fu">stats</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/stats/family.html" class="external-link">binomial</a></span><span class="op">(</span>link <span class="op">=</span> <span class="st">"logit"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">regression_table</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">gtsummary</span><span class="fu">::</span><span class="va"><a href="https://www.danieldsjoberg.com/gtsummary/reference/trial.html" class="external-link">trial</a></span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="regression_model.html">regression_model_uv</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> outcome.str <span class="op">=</span> <span class="st">"stage"</span>,</span></span>
<span class="r-in"><span> args.list <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>family <span class="op">=</span> <span class="fu">stats</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/stats/family.html" class="external-link">binomial</a></span><span class="op">(</span>link <span class="op">=</span> <span class="st">"logit"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">regression_table</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="st">"Univariable"</span> <span class="op">=</span> <span class="va">regression_model_uv</span>,</span></span>
<span class="r-in"><span> <span class="st">"Multivariable"</span> <span class="op">=</span> <span class="va">regression_model</span></span></span>
<span class="r-in"><span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span>\<span class="op">(</span><span class="va">.fun</span><span class="op">)</span><span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/do.call.html" class="external-link">do.call</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="va">.fun</span>,</span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>data <span class="op">=</span> <span class="fu">gtsummary</span><span class="fu">::</span><span class="va"><a href="https://www.danieldsjoberg.com/gtsummary/reference/trial.html" class="external-link">trial</a></span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>outcome.str <span class="op">=</span> <span class="st">"stage"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">}</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span><span class="va">regression_table</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="tbl_merge.html">tbl_merge</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span> <span class="co"># }</span></span></span>
<span class="r-in"><span><span class="va">regression_table</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="kw"><a href="https://rdrr.io/r/base/UseMethod.html" class="external-link">UseMethod</a></span><span class="op">(</span><span class="st">"regression_table"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co">#' @rdname regression_table</span></span></span>
<span class="r-in"><span><span class="co">#' @export</span></span></span>
<span class="r-in"><span><span class="va">regression_table.list</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">x</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">purrr</span><span class="fu">::</span><span class="fu"><a href="https://purrr.tidyverse.org/reference/map.html" class="external-link">map</a></span><span class="op">(</span>\<span class="op">(</span><span class="va">.m</span><span class="op">)</span><span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu">regression_table</span><span class="op">(</span>x <span class="op">=</span> <span class="va">.m</span>, <span class="va">...</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">gtsummary</span><span class="fu">::</span><span class="fu"><a href="https://www.danieldsjoberg.com/gtsummary/reference/add_n.html" class="external-link">add_n</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">}</span><span class="op">)</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">gtsummary</span><span class="fu">::</span><span class="fu"><a href="https://www.danieldsjoberg.com/gtsummary/reference/tbl_stack.html" class="external-link">tbl_stack</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co">#' @rdname regression_table</span></span></span>
<span class="r-in"><span><span class="co">#' @export</span></span></span>
<span class="r-in"><span><span class="va">regression_table.default</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, <span class="va">args.list</span> <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">fun</span> <span class="op">=</span> <span class="st">"gtsummary::tbl_regression"</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># Stripping custom class</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/class.html" class="external-link">class</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/class.html" class="external-link">class</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/class.html" class="external-link">class</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">!=</span> <span class="st">"freesearchr_model"</span><span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/class.html" class="external-link">class</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span> <span class="op">!=</span> <span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/class.html" class="external-link">class</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">!=</span> <span class="st">"lm"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="st">"exponentiate"</span> <span class="op"><a href="https://rdrr.io/r/base/match.html" class="external-link">%in%</a></span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">args.list</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">args.list</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">args.list</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>exponentiate <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">}</span></span></span>
<span class="r-in"><span> <span class="op">}</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="va">out</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/do.call.html" class="external-link">do.call</a></span><span class="op">(</span><span class="fu"><a href="getfun.html">getfun</a></span><span class="op">(</span><span class="va">fun</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">x</span><span class="op">)</span>, <span class="va">args.list</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="va">out</span> <span class="op">|&gt;</span></span></span>
<span class="r-in"><span> <span class="fu">gtsummary</span><span class="fu">::</span><span class="fu"><a href="https://www.danieldsjoberg.com/gtsummary/reference/add_glance.html" class="external-link">add_glance_source_note</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># |&gt;</span></span></span>
<span class="r-in"><span> <span class="co"># gtsummary::bold_p()</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
</code></pre></div>
</div> </div>
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2
search.json
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