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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title> Model Summary</title>
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<body>
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<div class="col-md-4" style="background:black;text-align:center"><a href="index.html" style="color:white"><i class="glyphicon glyphicon-th-list"></i> Back to index</a></div>
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<div class="container-fluid main-container">
<div id="model-summary" class="section level3 tab-content">
<h3>Model summary</h3>
<div id="full-summary" class="section level4">
<h4>Full summary</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">model_summary =<span class="st"> </span><span class="kw">summary</span>(model, <span class="dt">use_cache =</span> <span class="ot">FALSE</span>, <span class="dt">priors =</span> <span class="ot">TRUE</span>)
<span class="kw">print</span>(model_summary)</code></pre></div>
</div>
<div id="table-of-fixed-effects" class="section level4">
<h4>Table of fixed effects</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">fixed_eff =<span class="st"> </span><span class="kw">data.frame</span>(model_summary$fixed, <span class="dt">check.names =</span> F)
fixed_eff$Est.Error =<span class="st"> </span>fixed_eff$Eff.Sample =<span class="st"> </span>fixed_eff$Rhat =<span class="st"> </span><span class="ot">NULL</span>
fixed_eff$OR =<span class="st"> </span><span class="kw">exp</span>(fixed_eff$Estimate)
fixed_eff$OR_low =<span class="st"> </span><span class="kw">exp</span>(fixed_eff$<span class="st">`</span><span class="dt">l-95% CI</span><span class="st">`</span>)
fixed_eff$OR_high =<span class="st"> </span><span class="kw">exp</span>(fixed_eff$<span class="st">`</span><span class="dt">u-95% CI</span><span class="st">`</span>)
pander::<span class="kw">pander</span>(fixed_eff)</code></pre></div>
</div>
</div>
<div id="paternal-age-effect" class="section level3">
<h3>Paternal age effect</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">pander::<span class="kw">pander</span>(<span class="kw">paternal_age_10y_effect</span>(model))</code></pre></div>
</div>
<div id="marginal-effect-plots" class="section level3">
<h3>Marginal effect plots</h3>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">plot.brmsMarginalEffects_shades</span>(
<span class="dt">x =</span> <span class="kw">marginal_effects</span>(model, <span class="dt">re_formula =</span> <span class="ot">NA</span>, <span class="dt">probs =</span> <span class="kw">c</span>(<span class="fl">0.025</span>,<span class="fl">0.975</span>)),
<span class="dt">y =</span> <span class="kw">marginal_effects</span>(model, <span class="dt">re_formula =</span> <span class="ot">NA</span>, <span class="dt">probs =</span> <span class="kw">c</span>(<span class="fl">0.1</span>,<span class="fl">0.9</span>)),
<span class="dt">ask =</span> <span class="ot">FALSE</span>)</code></pre></div>
</div>
<div id="coefficient-plot" class="section level3">
<h3>Coefficient plot</h3>
<p>Coefficient estimates (95% and 80% credibility).</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">mcmc_intervals</span>(<span class="kw">as.matrix</span>(model$fit), <span class="dt">regex_pars =</span> <span class="st">"b_[^I]"</span>)
<span class="kw">mcmc_areas</span>(<span class="kw">as.matrix</span>(model$fit), <span class="dt">regex_pars =</span> <span class="st">"b"</span>)</code></pre></div>
</div>
<div id="diagnostics" class="section level3 tab-content">
<h3>Diagnostics</h3>
<p>These plots were made to diagnose misfit and nonconvergence.</p>
<div id="posterior-predictive-checks" class="section level4">
<h4>Posterior predictive checks</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">brms::<span class="kw">pp_check</span>(model, <span class="dt">re_formula =</span> <span class="ot">NA</span>, <span class="dt">type =</span> <span class="st">"dens_overlay"</span>)
brms::<span class="kw">pp_check</span>(model, <span class="dt">re_formula =</span> <span class="ot">NA</span>, <span class="dt">type =</span> <span class="st">"hist"</span>)</code></pre></div>
</div>
<div id="rhat" class="section level4">
<h4>Rhat</h4>
<p>Did the 6 chains converge?</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">stanplot</span>(model, <span class="dt">pars =</span> <span class="st">"^b_[^I]"</span>, <span class="dt">type =</span> <span class="st">'rhat'</span>)</code></pre></div>
</div>
<div id="effective-sample-size-by-average-sample-size" class="section level4">
<h4>Effective sample size by average sample size</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">stanplot</span>(model, <span class="dt">pars =</span> <span class="st">"^b"</span>, <span class="dt">type =</span> <span class="st">'ess'</span>)</code></pre></div>
</div>
<div id="monte-carlo-se" class="section level4">
<h4>Monte Carlo SE</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">stanplot</span>(model, <span class="dt">pars =</span> <span class="st">"^b"</span>, <span class="dt">type =</span> <span class="st">'mcse'</span>)</code></pre></div>
</div>
<div id="trace-plots" class="section level4">
<h4>Trace plots</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">if(<span class="kw">any</span>( <span class="kw">summary</span>(model)$fixed[,<span class="st">"Rhat"</span>] ><span class="st"> </span><span class="fl">1.1</span>)) { <span class="co"># only do traceplots if not converged</span>
<span class="kw">plot</span>(model, <span class="dt">N =</span> <span class="dv">3</span>, <span class="dt">ask =</span> <span class="ot">FALSE</span>)
}</code></pre></div>
</div>
<div id="further-plots" class="section level4">
<h4>Further plots</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">stanplot</span>(model, <span class="dt">pars =</span> <span class="st">"^b"</span>, <span class="dt">type =</span> <span class="st">'diag'</span>)</code></pre></div>
</div>
<div id="file-name" class="section level4">
<h4>File name</h4>
<p>MODEL_FILENAME</p>
</div>
<div id="cluster-script" class="section level4">
<h4>Cluster script</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">opts_chunk$<span class="kw">set</span>(<span class="dt">echo =</span> <span class="ot">FALSE</span>)
clusterscript =<span class="st"> </span><span class="kw">str_replace</span>(<span class="kw">basename</span>(model_filename), <span class="st">"</span><span class="ch">\\</span><span class="st">.rds"</span>,<span class="st">".html"</span>)
<span class="kw">cat</span>(<span class="st">"[Cluster script]("</span> , clusterscript, <span class="st">")"</span>, <span class="dt">sep =</span> <span class="st">""</span>)</code></pre></div>
</div>
</div>
</div>
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