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<title>Getting Started</title>
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<body>
<h1 class="title toc-ignore">Getting Started</h1>
<h4 class="date">2022-03-02</h4>
<div id="TOC">
<ul>
<li><a href="#using-the-shinystan-app-with-different-types-of-objects">Using the ShinyStan app with different types of objects</a>
<ul>
<li><a href="#stanfit-objects">stanfit objects</a>
<ul>
<li><a href="#stanreg-and-brmsfit-objects">stanreg and brmsfit objects</a></li>
</ul></li>
<li><a href="#mcmc.list-objects">mcmc.list objects</a></li>
<li><a href="#other-types-of-objects">Other types of objects</a>
<ul>
<li><a href="#d-array">3-D array</a></li>
<li><a href="#list-of-matrices">List of matrices</a></li>
</ul></li>
</ul></li>
<li><a href="#other-functions-in-the-shinystan-package">Other functions in the shinystan package</a>
<ul>
<li><a href="#generating-new-quantities">Generating new quantities</a></li>
<li><a href="#storing-your-model-code-in-a-shinystan-object">Storing your model code in a shinystan object</a></li>
<li><a href="#renaming-a-model">Renaming a model</a></li>
</ul></li>
</ul>
</div>
<div id="using-the-shinystan-app-with-different-types-of-objects" class="section level1">
<h1>Using the ShinyStan app with different types of objects</h1>
<div id="stanfit-objects" class="section level2">
<h2>stanfit objects</h2>
<p>If <code>my_stanfit</code> is a stanfit object (the result of fitting a model with <a href="https://mc-stan.org/"><strong>rstan</strong></a>), then to launch the ShinyStan app simply use</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(shinystan)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>my_sso <span class="ot"><-</span> <span class="fu">launch_shinystan</span>(my_stanfit)</span></code></pre></div>
<p>and ShinyStan will launch. Here <code>my_sso</code> is the name you want to use for the shinystan object that will be returned. If you simply run</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">launch_shinystan</span>(my_stanfit)</span></code></pre></div>
<p>then ShinyStan will launch but no shinystan object will be saved upon quitting the app.</p>
<p>Sometimes keeping only a subset of parameters before can improve performance. This can be done by creating an object with <code>as.shinystan</code> and specifying the <code>pars</code> argument. The resulting shinystan object can then be passed to <code>launch_shinystan()</code>.</p>
<div id="stanreg-and-brmsfit-objects" class="section level3">
<h3>stanreg and brmsfit objects</h3>
<p>The <strong>rstanarm</strong> and <strong>brms</strong> packages provide <code>launch_shinystan</code> methods for stanreg and brmsfit objects, respectively. For example, the method for stanreg objects is documented at</p>
<p><a href="http://mc-stan.org/rstanarm/reference/launch_shinystan.stanreg.html" class="uri">http://mc-stan.org/rstanarm/reference/launch_shinystan.stanreg.html</a></p>
</div>
</div>
<div id="mcmc.list-objects" class="section level2">
<h2>mcmc.list objects</h2>
<p>If you have an <code>mcmc.list</code> object called <code>my_mcmc</code> then you can use the <code>as.shinystan</code> function to convert <code>my_mcmc</code> into a shinystan object that can then be used with <code>launch_shinystan</code>:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>my_sso <span class="ot"><-</span> <span class="fu">launch_shinystan</span>(<span class="fu">as.shinystan</span>(my_mcmc, <span class="at">model_name =</span> <span class="st">"my_model"</span>))</span></code></pre></div>
<p>If, for example, the first 100 iterations in each chain in <code>my_mcmc</code> are warmup iterations, you should add the <code>warmup</code> argument when you call <code>as.shinystan</code>:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>my_sso <span class="ot"><-</span> <span class="fu">launch_shinystan</span>(<span class="fu">as.shinystan</span>(my_mcmc, <span class="at">model_name =</span> <span class="st">"my_model"</span>, <span class="at">warmup =</span> <span class="dv">100</span>))</span></code></pre></div>
<p>However, you should only use the <code>warmup</code> argument if the warmup iterations have been saved and included in <code>my_mcmc</code>.</p>
</div>
<div id="other-types-of-objects" class="section level2">
<h2>Other types of objects</h2>
<div id="d-array" class="section level3">
<h3>3-D array</h3>
<p>To convert a 3-D array to a shinystan object make sure that the three dimensions of the array correspond to the <em>number of iterations</em> <strong>x</strong> <em>number of chains</em> <strong>x</strong> <em>number of parameters</em>. You can then <code>as.shinystan</code> exactly how it’s used in the examples for <code>mcmc.list</code> objects above (but you don’t need to convert your array to an <code>mcmc.list</code>).</p>
</div>
<div id="list-of-matrices" class="section level3">
<h3>List of matrices</h3>
<p>If you have separate chains that are each a matrix (with iterations as rows and parameters as columns) you can combine them in a list to pass to <code>as.shinystan</code></p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Generate some fake data</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>chain1 <span class="ot"><-</span> <span class="fu">cbind</span>(<span class="at">beta1 =</span> <span class="fu">rnorm</span>(<span class="dv">100</span>), <span class="at">beta2 =</span> <span class="fu">rnorm</span>(<span class="dv">100</span>), <span class="at">sigma =</span> <span class="fu">rexp</span>(<span class="dv">100</span>))</span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>chain2 <span class="ot"><-</span> <span class="fu">cbind</span>(<span class="at">beta1 =</span> <span class="fu">rnorm</span>(<span class="dv">100</span>), <span class="at">beta2 =</span> <span class="fu">rnorm</span>(<span class="dv">100</span>), <span class="at">sigma =</span> <span class="fu">rexp</span>(<span class="dv">100</span>))</span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>chain_list <span class="ot"><-</span> <span class="fu">list</span>(chain1, chain2)</span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>my_sso <span class="ot"><-</span> <span class="fu">launch_shinystan</span>(<span class="fu">as.shinystan</span>(<span class="at">X =</span> <span class="fu">list</span>(chain1, chain2), <span class="at">model_name =</span> <span class="st">"my_model"</span>))</span></code></pre></div>
<hr />
</div>
</div>
</div>
<div id="other-functions-in-the-shinystan-package" class="section level1">
<h1>Other functions in the shinystan package</h1>
<div id="generating-new-quantities" class="section level2">
<h2>Generating new quantities</h2>
<p>You can add a new parameter/quantity as a function of one or two existing parameters to your shinystan object by using the <code>generate_quantity</code> function. For example, assume <code>sso</code> is a shinystan object and two of the parameters are <code>alpha</code> and <code>beta</code>. We could add a parameter <code>gamma</code> that is the inverse logit of <code>beta</code> using the code</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>inv_logit <span class="ot"><-</span> <span class="cf">function</span>(x) <span class="dv">1</span><span class="sc">/</span>(<span class="dv">1</span> <span class="sc">+</span> <span class="fu">exp</span>(<span class="sc">-</span>x))</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>sso <span class="ot"><-</span> <span class="fu">generate_quantity</span>(sso, <span class="at">fun =</span> inv_logit, <span class="at">param1 =</span> <span class="st">"beta"</span>, <span class="at">new_name =</span> <span class="st">"gamma"</span>)</span></code></pre></div>
<p>Here, <code>fun</code> is the function we want to use, <code>param1</code> is the name of the parameter to apply the function to, and <code>new_name</code> is the name to give the new parameter.</p>
<p>Adding a parameter as a function of two parameters just requires specifying the <code>param2</code> argument and providing a function of two variables. For example, we can add a parameter <code>delta</code> to <code>sso</code> that is the squared difference of <code>alpha</code> and <code>beta</code> like this</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>sso <span class="ot"><-</span> <span class="fu">generate_quantity</span>(sso, <span class="at">fun =</span> <span class="cf">function</span>(x,y) (x<span class="sc">-</span>y)<span class="sc">^</span><span class="dv">2</span>,</span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="at">param1 =</span> <span class="st">"alpha"</span>, <span class="at">param2 =</span> <span class="st">"beta"</span>, <span class="at">new_name =</span> <span class="st">"delta"</span>)</span></code></pre></div>
</div>
<div id="storing-your-model-code-in-a-shinystan-object" class="section level2">
<h2>Storing your model code in a shinystan object</h2>
<p>For models fit using <strong>rstan</strong> the model code will automatically be stored in the <code>model_code</code> slot of your shinystan object. When ShinyStan is open you can view your model code in the <em>Model Code</em> tab.</p>
<p>If you did not use <strong>rstan</strong> fit your model then you can add your model code by using the <code>model_code()</code> function. For example, you may have used Bugs or JAGS or some other software and want to add the following code</p>
<pre><code> for (i in 1:length(Y)) {
Y[i] ~ dpois(lambda[i])
log(lambda[i]) <- inprod(X[i,], theta[])
}
for (j in 1:J) {
theta[j] ~ dt(0.0, 1.0, 1.0)
}
}</code></pre>
<p>to your shinystan object. To add that code you can simply include it as the <code>code</code> argument to the <code>model_code</code> function</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>my_code <span class="ot"><-</span> <span class="st">"</span></span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="st"> model {</span></span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="st"> for (i in 1:length(Y)) {</span></span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a><span class="st"> Y[i] ~ dpois(lambda[i])</span></span>
<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a><span class="st"> log(lambda[i]) <- inprod(X[i,], theta[])</span></span>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a><span class="st"> }</span></span>
<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a><span class="st"> for (j in 1:J) {</span></span>
<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a><span class="st"> theta[j] ~ dt(0.0, 1.0, 1.0)</span></span>
<span id="cb9-9"><a href="#cb9-9" aria-hidden="true" tabindex="-1"></a><span class="st"> }</span></span>
<span id="cb9-10"><a href="#cb9-10" aria-hidden="true" tabindex="-1"></a><span class="st"> }</span></span>
<span id="cb9-11"><a href="#cb9-11" aria-hidden="true" tabindex="-1"></a><span class="st">"</span></span>
<span id="cb9-12"><a href="#cb9-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb9-13"><a href="#cb9-13" aria-hidden="true" tabindex="-1"></a><span class="co"># Add the code to a shinystan object sso</span></span>
<span id="cb9-14"><a href="#cb9-14" aria-hidden="true" tabindex="-1"></a>sso <span class="ot"><-</span> <span class="fu">model_code</span>(sso, <span class="at">code =</span> my_code)</span></code></pre></div>
</div>
<div id="renaming-a-model" class="section level2">
<h2>Renaming a model</h2>
<p>On the home page ShinyStan will display the model name associated with the shinystan object being used. This name can be set by adding the <code>model_name</code> argument to <code>as.shinystan</code> when creating a shinystan object. For an existing shinystan object you can use the <code>model_name</code> function like this:</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>sso <span class="ot"><-</span> <span class="fu">model_name</span>(sso, <span class="st">"new_model_name"</span>)</span></code></pre></div>
<p>where <code>"new_model_name"</code> is the new name you want to give your model.</p>
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