New Upstream Snapshot - r-cran-shinystan
Ready changes
Summary
Merged new upstream version: 2.6.0+git20220804.1.f8ec132 (was: 2.6.0).
Resulting package
Built on 2023-02-08T13:37 (took 8m57s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots r-cran-shinystan
Lintian Result
Diff
diff --git a/DESCRIPTION b/DESCRIPTION
index be5e010..e1e06ba 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,7 +26,7 @@ Description: A graphical user interface for interactive Markov chain Monte
packages).
URL: https://mc-stan.org/shinystan/, https://discourse.mc-stan.org
BugReports: https://github.com/stan-dev/shinystan/issues/
-License: GPL (>= 3)
+License: GPL (>=3)
Depends: R (>= 3.1.0), shiny (>= 1.0.3)
Imports: bayesplot (>= 1.5.0), colourpicker, DT (>= 0.2), dygraphs (>=
1.1.1.2), ggplot2 (>= 2.1.1), gridExtra, gtools, markdown (>=
@@ -42,7 +42,7 @@ Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 7.1.2
NeedsCompilation: no
-Packaged: 2022-03-02 19:40:48 UTC; jgabry
+Packaged: 2023-02-08 13:33:43 UTC; janitor
Author: Jonah Gabry [aut, cre],
Duco Veen [aut],
Stan Development Team [ctb],
@@ -55,5 +55,3 @@ Author: Jonah Gabry [aut, cre],
Daniel Lee [ctb],
Dongying Song [ctb],
Rob Trangucci [ctb]
-Repository: CRAN
-Date/Publication: 2022-03-03 00:10:02 UTC
diff --git a/MD5 b/MD5
deleted file mode 100644
index 39421ee..0000000
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+++ /dev/null
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diff --git a/build/vignette.rds b/build/vignette.rds
index 00bdd26..145af21 100644
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diff --git a/debian/changelog b/debian/changelog
index 0dd4743..a8a27ce 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,12 @@
-r-cran-shinystan (2.6.0-2) UNRELEASED; urgency=medium
+r-cran-shinystan (2.6.0+git20220804.1.f8ec132-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Disable reprotest
- -- Andreas Tille <tille@debian.org> Fri, 11 Mar 2022 12:10:43 +0100
+ [ Debian Janitor ]
+ * New upstream snapshot.
+
+ -- Andreas Tille <tille@debian.org> Wed, 08 Feb 2023 13:33:48 -0000
r-cran-shinystan (2.6.0-1) unstable; urgency=medium
diff --git a/inst/doc/deploy_shinystan.html b/inst/doc/deploy_shinystan.html
index bf5ddf9..6454598 100644
--- a/inst/doc/deploy_shinystan.html
+++ b/inst/doc/deploy_shinystan.html
@@ -15,7 +15,19 @@
<title>Deploying to shinyapps.io</title>
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code span.fu { color: #06287e; } /* Function */
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+code span.im { color: #008000; font-weight: bold; } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
@@ -108,13 +121,20 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
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try { var rules = sheets[i].cssRules; } catch (e) { continue; }
- for (var j = 0; j < rules.length; j++) {
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+ while (j < rules.length) {
var rule = rules[j];
// check if there is a div.sourceCode rule
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+ if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") {
+ j++;
+ continue;
+ }
var style = rule.style.cssText;
// check if color or background-color is set
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+ if (rule.style.color === '' && rule.style.backgroundColor === '') {
+ j++;
+ continue;
+ }
// replace div.sourceCode by a pre.sourceCode rule
sheets[i].deleteRule(j);
sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
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@@ -143,40 +343,74 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
-<p>Create a ShinyStan app unique to your model and host it online with RStudio’s ShinyApps service (shinyapps.io). Each app you deploy will have a unique url.</p>
-<p><em>Note: R users who don’t use RStudio’s IDE can still deploy ShinyStan apps to shinyapps.io.</em></p>
+<p>Create a ShinyStan app unique to your model and host it online with
+RStudio’s ShinyApps service (shinyapps.io). Each app you deploy will
+have a unique url.</p>
+<p><em>Note: R users who don’t use RStudio’s IDE can still deploy
+ShinyStan apps to shinyapps.io.</em></p>
<div id="step-1-shinyapps-account" class="section level2">
<h2>Step 1: ShinyApps account</h2>
<p><strong>Signup</strong></p>
-<p>To deploy your app to RStudio’s shinyapps.io you will need a ShinyApps account. If you don’t already have one you can sign up at <a href="https://www.shinyapps.io/" class="uri">https://www.shinyapps.io/</a>.</p>
-<p>The only limit to the number of different ShinyStan apps you can deploy is the limit set by RStudio for the <a href="https://www.shinyapps.io/#pricing">type of ShinyApps account</a> you sign up for.</p>
+<p>To deploy your app to RStudio’s shinyapps.io you will need a
+ShinyApps account. If you don’t already have one you can sign up at <a href="https://www.shinyapps.io/" class="uri">https://www.shinyapps.io/</a>.</p>
+<p>The only limit to the number of different ShinyStan apps you can
+deploy is the limit set by RStudio for the <a href="https://www.shinyapps.io/#pricing">type of ShinyApps account</a>
+you sign up for.</p>
<p><strong>Setup</strong></p>
-<p>When you finish signing up for your ShinyApps account there will be instructions for setting up your account on your local system using <code>rsconnect::setAccountInfo()</code> (this requires first installing the <strong>rsconnect</strong> package)</p>
+<p>When you finish signing up for your ShinyApps account there will be
+instructions for setting up your account on your local system using
+<code>rsconnect::setAccountInfo()</code> (this requires first installing
+the <strong>rsconnect</strong> package)</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>rsconnect<span class="sc">::</span><span class="fu">setAccountInfo</span>(name, token, secret)</span></code></pre></div>
-<p>where <code>name</code> is your ShinyApps account name, and <code>token</code> and <code>secret</code> can be found from your ShinyApps account web page.</p>
+<p>where <code>name</code> is your ShinyApps account name, and
+<code>token</code> and <code>secret</code> can be found from your
+ShinyApps account web page.</p>
</div>
<div id="step-2-use-deploy_shinystan-to-deploy-your-app-to-shinyapps.io" class="section level2">
-<h2>Step 2: Use <code>deploy_shinystan</code> to deploy your app to shinyapps.io</h2>
-<p>The <code>deploy_shinystan</code> function will deploy a ShinyStan app unique to your model to RStudio’s ShinyApps service.</p>
+<h2>Step 2: Use <code>deploy_shinystan</code> to deploy your app to
+shinyapps.io</h2>
+<p>The <code>deploy_shinystan</code> function will deploy a ShinyStan
+app unique to your model to RStudio’s ShinyApps service.</p>
<p>For the example below assume that</p>
<ul>
<li><code>my_sso</code> is the shinystan object you want to use</li>
<li>the name you want to use for the app is <code>MyModel</code></li>
-<li>the username for your ShinyApps account (from Step 1) is <code>username</code>.</li>
+<li>the username for your ShinyApps account (from Step 1) is
+<code>username</code>.</li>
</ul>
<p>To deploy the app use the command</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">deploy_shinystan</span>(my_sso, <span class="at">appName =</span> <span class="st">"MyModel"</span>, <span class="at">account =</span> <span class="st">"username"</span>)</span></code></pre></div>
-<p><strong>When to specify the <code>account</code> argument</strong></p>
-<p>If you have multiple ShinyApps accounts configured on your local system then the <code>account</code> argument is required. If you only have a single account then you can omit <code>account</code></p>
+<p><strong>When to specify the <code>account</code>
+argument</strong></p>
+<p>If you have multiple ShinyApps accounts configured on your local
+system then the <code>account</code> argument is required. If you only
+have a single account then you can omit <code>account</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><span class="fu">deploy_shinystan</span>(my_sso, <span class="at">appName =</span> <span class="st">"MyModel"</span>)</span></code></pre></div>
-<p><strong>Graphical posterior predictive checks: the optional <code>ppcheck_data</code> and <code>ppcheck_yrep</code> arguments</strong></p>
-<p>If you have a vector of observations <code>y</code> that you want to use for ShinyStan’s graphical posterior predictive checks then you can also specify the optional <code>ppcheck_data</code> argument</p>
+<p><strong>Graphical posterior predictive checks: the optional
+<code>ppcheck_data</code> and <code>ppcheck_yrep</code>
+arguments</strong></p>
+<p>If you have a vector of observations <code>y</code> that you want to
+use for ShinyStan’s graphical posterior predictive checks then you can
+also specify the optional <code>ppcheck_data</code> argument</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><span class="fu">deploy_shinystan</span>(my_sso, <span class="at">appName =</span> <span class="st">"MyModel"</span>, </span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="at">ppcheck_data =</span> y)</span></code></pre></div>
-<p>If you’ve specified the <code>ppcheck_data</code> argument you can also use the <code>ppcheck_yrep</code> argument to tell ShinyStan the name of the parameter/quantity in your model containing the posterior predictive simulations/replications so that it is preselected as the parameter to use for doing the graphical posterior predictive checks. This is never required because you can also set this manually while using the app, but it is helpful if you want other people to view your model online because it avoids the need to communicate to them which parameter they need to select. If this parameter/quantity containing the posterior predictive replications is named <code>yRep</code> then you would use</p>
+<p>If you’ve specified the <code>ppcheck_data</code> argument you can
+also use the <code>ppcheck_yrep</code> argument to tell ShinyStan the
+name of the parameter/quantity in your model containing the posterior
+predictive simulations/replications so that it is preselected as the
+parameter to use for doing the graphical posterior predictive checks.
+This is never required because you can also set this manually while
+using the app, but it is helpful if you want other people to view your
+model online because it avoids the need to communicate to them which
+parameter they need to select. If this parameter/quantity containing the
+posterior predictive replications is named <code>yRep</code> then you
+would use</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="fu">deploy_shinystan</span>(my_sso, <span class="at">appName =</span> <span class="st">"MyModel"</span>, </span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="at">ppcheck_data =</span> y, <span class="at">ppcheck_yrep =</span> <span class="st">"yRep"</span>)</span></code></pre></div>
-<p>If the deployment process is successful the url for your app will be printed to the console and it should open in your web browser. You can also view your app by going to <a href="https://www.shinyapps.io" class="uri">https://www.shinyapps.io</a> and logging into your account.</p>
+<p>If the deployment process is successful the url for your app will be
+printed to the console and it should open in your web browser. You can
+also view your app by going to <a href="https://www.shinyapps.io" class="uri">https://www.shinyapps.io</a> and logging into your
+account.</p>
</div>
diff --git a/inst/doc/shinystan-package.html b/inst/doc/shinystan-package.html
index 18cf263..a49bcc8 100644
--- a/inst/doc/shinystan-package.html
+++ b/inst/doc/shinystan-package.html
@@ -11,11 +11,23 @@
<meta name="viewport" content="width=device-width, initial-scale=1" />
-<meta name="date" content="2022-03-02" />
+<meta name="date" content="2023-02-08" />
<title>Getting Started</title>
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code{white-space: pre-wrap;}
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code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
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@@ -139,16 +339,18 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
<h1 class="title toc-ignore">Getting Started</h1>
-<h4 class="date">2022-03-02</h4>
+<h4 class="date">2023-02-08</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>
+<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>
+<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>
@@ -157,10 +359,13 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
<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>
+<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="#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>
@@ -170,36 +375,64 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
<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>
+<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>
+<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>
+<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>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>
+<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>
+<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>
+<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>
+<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>
+<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>
@@ -213,18 +446,36 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
<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>
+<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>
+<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>
+<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[])
@@ -233,7 +484,9 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
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>
+<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>
@@ -251,9 +504,14 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
</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>
+<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>
+<p>where <code>"new_model_name"</code> is the new name you want to give
+your model.</p>
</div>
</div>
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Debdiff
[The following lists of changes regard files as different if they have different names, permissions or owners.]
Files in second set of .debs but not in first
-rw-r--r-- root/root /usr/lib/R/site-library/shinystan/help/figures/logo.svg
No differences were encountered in the control files