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26 changed files with 1564 additions and 183 deletions
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@ -1,5 +1,5 @@
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<!DOCTYPE html>
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create a regression model programatically — regression_model • freesearcheR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Montserrat-0.4.9/font.css" rel="stylesheet"><link href="../deps/Public_Sans-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Create a regression model programatically — regression_model"><meta name="description" content="Create a regression model programatically"><meta property="og:description" content="Create a regression model programatically"></head><body>
|
||||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create a regression model programatically — regression_model • freesearcheR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Montserrat-0.4.9/font.css" rel="stylesheet"><link href="../deps/Public_Sans-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><meta property="og:title" content="Create a regression model programatically — regression_model"><meta name="description" content="Output is a concatenated list of model information and model"><meta property="og:description" content="Output is a concatenated list of model information and model"></head><body>
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<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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@ -35,7 +35,7 @@
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</div>
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<div class="ref-description section level2">
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<p>Create a regression model programatically</p>
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<p>Output is a concatenated list of model information and model</p>
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</div>
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<div class="section level2">
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@ -43,12 +43,43 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">regression_model</span><span class="op">(</span></span>
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<span> <span class="va">data</span>,</span>
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<span> <span class="va">outcome.str</span>,</span>
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<span> auto.mode <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> auto.mode <span class="op">=</span> <span class="cn">FALSE</span>,</span>
|
||||
<span> formula.str <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||||
<span> args.list <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
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<span> fun <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> vars <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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||||
<span></span>
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<span><span class="fu">regression_model_uv</span><span class="op">(</span></span>
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<span> <span class="va">data</span>,</span>
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<span> <span class="va">outcome.str</span>,</span>
|
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<span> args.list <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
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<span> fun <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
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<span> vars <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">regression_model_list</span><span class="op">(</span></span>
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<span> <span class="va">data</span>,</span>
|
||||
<span> <span class="va">outcome.str</span>,</span>
|
||||
<span> <span class="va">fun.descr</span>,</span>
|
||||
<span> fun <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||||
<span> formula.str <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||||
<span> args.list <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||||
<span> vars <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||||
<span> <span class="va">...</span></span>
|
||||
<span><span class="op">)</span></span>
|
||||
<span></span>
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<span><span class="fu">regression_model_uv_list</span><span class="op">(</span></span>
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<span> <span class="va">data</span>,</span>
|
||||
<span> <span class="va">outcome.str</span>,</span>
|
||||
<span> <span class="va">fun.descr</span>,</span>
|
||||
<span> fun <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
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<span> formula.str <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||||
<span> args.list <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||||
<span> vars <span class="op">=</span> <span class="cn">NULL</span>,</span>
|
||||
<span> <span class="va">...</span></span>
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||||
<span><span class="op">)</span></span></code></pre></div>
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</div>
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@ -57,11 +88,11 @@
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|
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<dl><dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt>
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<dd><p>data set</p></dd>
|
||||
<dd><p>data</p></dd>
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||||
|
||||
|
||||
<dt id="arg-outcome-str">outcome.str<a class="anchor" aria-label="anchor" href="#arg-outcome-str"></a></dt>
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||||
<dd><p>Name of outcome variable. Character vector.</p></dd>
|
||||
<dd><p>name of outcome variable</p></dd>
|
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|
||||
|
||||
<dt id="arg-auto-mode">auto.mode<a class="anchor" aria-label="anchor" href="#arg-auto-mode"></a></dt>
|
||||
|
|
@ -69,15 +100,16 @@
|
|||
|
||||
|
||||
<dt id="arg-formula-str">formula.str<a class="anchor" aria-label="anchor" href="#arg-formula-str"></a></dt>
|
||||
<dd><p>Formula as string. Passed through 'glue::glue'. If given, 'outcome.str' and 'vars' are ignored. Optional.</p></dd>
|
||||
<dd><p>custom formula glue string. Default is NULL.</p></dd>
|
||||
|
||||
|
||||
<dt id="arg-args-list">args.list<a class="anchor" aria-label="anchor" href="#arg-args-list"></a></dt>
|
||||
<dd><p>List of arguments passed to 'fun' with 'do.call'.</p></dd>
|
||||
<dd><p>custom character string to be converted using
|
||||
argsstring2list() or list of arguments. Default is NULL.</p></dd>
|
||||
|
||||
|
||||
<dt id="arg-fun">fun<a class="anchor" aria-label="anchor" href="#arg-fun"></a></dt>
|
||||
<dd><p>Name of function as character vector or function to use for model creation.</p></dd>
|
||||
<dd><p>name of custom function. Default is NULL.</p></dd>
|
||||
|
||||
|
||||
<dt id="arg-vars">vars<a class="anchor" aria-label="anchor" href="#arg-vars"></a></dt>
|
||||
|
|
@ -85,12 +117,20 @@
|
|||
|
||||
|
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<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
|
||||
<dd><p>ignored for now</p></dd>
|
||||
<dd><p>ignored</p></dd>
|
||||
|
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|
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<dt id="arg-fun-descr">fun.descr<a class="anchor" aria-label="anchor" href="#arg-fun-descr"></a></dt>
|
||||
<dd><p>Description of chosen function matching description in
|
||||
"supported_functions()"</p></dd>
|
||||
|
||||
</dl></div>
|
||||
<div class="section level2">
|
||||
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
|
||||
<p>object of standard class for fun</p>
|
||||
<p>object of standard class for fun</p>
|
||||
<p>list</p>
|
||||
<p>list</p>
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
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|
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@ -524,12 +564,14 @@
|
|||
<span class="r-out co"><span class="r-pr">#></span> gradeII gradeIII response death ttdeath </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 0.1750 1.6855 4.9885 3.0775 -0.1394 </span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
|
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<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">|></span> <span class="fu">regression_model</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> auto.mode <span class="op">=</span> <span class="cn">FALSE</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></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">|></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="default_parsing.html">default_parsing</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">regression_model</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> auto.mode <span class="op">=</span> <span class="cn">FALSE</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></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Call: (function (formula, family = gaussian, data, weights, subset, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> na.action, start = NULL, etastart, mustart, offset, control = list(...), </span>
|
||||
|
|
@ -765,35 +807,36 @@
|
|||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 2L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3L, 1L, 2L, 1L, 1L, 3L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 2L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3L, 2L, 3L, 3L, 2L, 1L, 2L, 3L, 3L, 1L), levels = c("I", </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "II", "III"), class = "factor", label = "Grade"), response = structure(c(0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 0L, 1L, 0L, NA, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, 1L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 0L, 0L, NA, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, 0L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, NA, 1L, 1L, 1L, 0L, 1L, 0L, 0L, 1L, 0L, NA, 1L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 1L, 1L, 0L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 1L, NA, 0L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 0L, 1L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, NA, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 0L, 0L), label = "Tumor Response"), death = structure(c(0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 0L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 1L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 1L, 0L, 0L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 0L, 0L, 1L, 1L, 0L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 1L, 1L, 1L, 0L, 1L, 1L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, 1L, 1L, 0L, 0L, 0L, 1L, 0L, 1L, 0L, 1L, 1L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 0L, 1L, 1L, 0L, 0L, 1L, 1L, 1L, 1L, 0L, 1L, 0L, 1L, 1L, 0L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 0L, 1L, 0L), label = "Patient Died"), ttdeath = structure(c(24, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "II", "III"), class = "factor", label = "Grade"), response = structure(c(1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 2L, 1L, NA, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, NA, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L, 1L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2L, 2L, NA, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, NA, 2L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, NA, 1L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, NA, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2L, 2L, 1L, 1L), levels = c("0", "1"), class = "factor", label = "Tumor Response"), </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> death = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1L, 2L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 1L), levels = c("0", </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "1"), class = "factor", label = "Patient Died"), ttdeath = structure(c(24, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 24, 24, 17.64, 16.43, 15.64, 24, 18.43, 24, 10.53, 24, 24, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 14.34, 12.89, 22.68, 8.71, 24, 15.21, 24, 24, 24, 24, 16.92, </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 23.89, 6.32, 15.77, 24, 24, 15.45, 17.43, 24, 20.9, 24, 24, </span>
|
||||
|
|
@ -818,13 +861,80 @@
|
|||
<span class="r-out co"><span class="r-pr">#></span> Coefficients:</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (Intercept) age marker stageT2 stageT3 stageT4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1.652845 -0.002014 -0.259849 0.404341 0.117402 -0.002102 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> gradeII gradeIII response death ttdeath </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> gradeII gradeIII response1 death1 ttdeath </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> -0.037012 0.022890 0.498952 -0.003916 -0.076073 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Degrees of Freedom: 172 Total (i.e. Null); 162 Residual</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> (27 observations deleted due to missingness)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Null Deviance: 239.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Residual Deviance: 230.9 AIC: 252.9</span>
|
||||
<span class="r-in"><span><span class="va">m</span> <span class="op"><-</span> <span class="va">mtcars</span> <span class="op">|></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="default_parsing.html">default_parsing</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">regression_model</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> outcome.str <span class="op">=</span> <span class="st">"mpg"</span>,</span></span>
|
||||
<span class="r-in"><span> auto.mode <span class="op">=</span> <span class="cn">FALSE</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}~{paste(vars,collapse='+')}"</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> vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mpg"</span>, <span class="st">"cyl"</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="fu">broom</span><span class="fu">::</span><span class="fu"><a href="https://generics.r-lib.org/reference/tidy.html" class="external-link">tidy</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> term estimate std.error statistic p.value</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> (Intercept) 26.7 0.972 27.4 2.69<span style="color: #949494;">e</span><span style="color: #BB0000;">-22</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> cyl6 -<span style="color: #BB0000;">6.92</span> 1.56 -<span style="color: #BB0000;">4.44</span> 1.19<span style="color: #949494;">e</span><span style="color: #BB0000;">- 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> cyl8 -<span style="color: #BB0000;">11.6</span> 1.30 -<span style="color: #BB0000;">8.90</span> 8.57<span style="color: #949494;">e</span><span style="color: #BB0000;">-10</span></span>
|
||||
<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="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">regression_model_uv</span><span class="op">(</span>outcome.str <span class="op">=</span> <span class="st">"age"</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">|></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">regression_model_uv</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> args.list <span class="op">=</span> <span class="cn">NULL</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">m</span> <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 class="fu">regression_model_uv</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></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="va">m</span>,<span class="fu">broom</span><span class="fu">::</span><span class="va"><a href="https://generics.r-lib.org/reference/tidy.html" class="external-link">tidy</a></span><span class="op">)</span> <span class="op">|></span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows</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="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="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">regression_model</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></span>
|
||||
<span class="r-in"><span><span class="va">ls</span> <span class="op"><-</span> <span class="fu">regression_model_list</span><span class="op">(</span>data <span class="op">=</span> <span class="fu"><a href="default_parsing.html">default_parsing</a></span><span class="op">(</span><span class="va">mtcars</span><span class="op">)</span>, outcome.str <span class="op">=</span> <span class="st">"cyl"</span>, fun.descr <span class="op">=</span> <span class="st">"Ordinal logistic regression model"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">ls</span><span class="op">$</span><span class="va">model</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="va">ls</span> <span class="op"><-</span> <span class="fu">regression_model_list</span><span class="op">(</span>data <span class="op">=</span> <span class="fu"><a href="default_parsing.html">default_parsing</a></span><span class="op">(</span><span class="fu">gtsummary</span><span class="fu">::</span><span class="va"><a href="https://www.danieldsjoberg.com/gtsummary/reference/trial.html" class="external-link">trial</a></span><span class="op">)</span>, outcome.str <span class="op">=</span> <span class="st">"trt"</span>, fun.descr <span class="op">=</span> <span class="st">"Logistic regression model"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">tbl</span> <span class="op"><-</span> <span class="fu">gtsummary</span><span class="fu">::</span><span class="fu"><a href="https://www.danieldsjoberg.com/gtsummary/reference/tbl_regression.html" class="external-link">tbl_regression</a></span><span class="op">(</span><span class="va">ls</span><span class="op">$</span><span class="va">model</span>, exponentiate <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">m</span> <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="default_parsing.html">default_parsing</a></span><span class="op">(</span><span class="op">)</span> <span class="op">|></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu">regression_model</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> 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="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></span>
|
||||
<span class="r-in"><span><span class="va">tbl2</span> <span class="op"><-</span> <span class="fu">gtsummary</span><span class="fu">::</span><span class="fu"><a href="https://www.danieldsjoberg.com/gtsummary/reference/tbl_regression.html" class="external-link">tbl_regression</a></span><span class="op">(</span><span class="va">m</span>, exponentiate <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">broom</span><span class="fu">::</span><span class="fu"><a href="https://generics.r-lib.org/reference/tidy.html" class="external-link">tidy</a></span><span class="op">(</span><span class="va">ls</span><span class="op">$</span><span class="va">model</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">broom</span><span class="fu">::</span><span class="fu"><a href="https://generics.r-lib.org/reference/tidy.html" class="external-link">tidy</a></span><span class="op">(</span><span class="va">m</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="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="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 class="fu">regression_model_uv</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">|></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="fu">broom</span><span class="fu">::</span><span class="va"><a href="https://generics.r-lib.org/reference/tidy.html" class="external-link">tidy</a></span><span class="op">)</span> <span class="op">|></span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">ms</span> <span class="op"><-</span> <span class="fu">regression_model_uv_list</span><span class="op">(</span>data <span class="op">=</span> <span class="fu"><a href="default_parsing.html">default_parsing</a></span><span class="op">(</span><span class="va">mtcars</span><span class="op">)</span>, outcome.str <span class="op">=</span> <span class="st">"mpg"</span>, fun.descr <span class="op">=</span> <span class="st">"Linear regression model"</span><span class="op">)</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="va">ms</span><span class="op">$</span><span class="va">model</span>,<span class="fu">broom</span><span class="fu">::</span><span class="va"><a href="https://generics.r-lib.org/reference/tidy.html" class="external-link">tidy</a></span><span class="op">)</span> <span class="op">|></span> <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows</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>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
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