density_plot

Used by <code>diag_plots()</code>, not intended to be called separately

The aim of 'postpack' is to provide the infrastructure for a standardized workflow for 'mcmc.list' objects.
These objects can be used to store output from models fitted with Bayesian inference using
'JAGS', 'WinBUGS', 'OpenBUGS', 'NIMBLE', 'Stan', or even custom MCMC algorithms. Although the 'coda' R package provides
some methods for these objects, it is somewhat limited in easily performing post-processing tasks for
specific nodes. Models are ever increasing in their complexity and the number of tracked nodes, and oftentimes
a user may wish to summarize/diagnose sampling behavior for only a small subset of nodes at a time
for a particular question or figure. Thus, many 'postpack' functions support performing tasks on a
subset of nodes, where the subset is specified with regular expressions. The functions in 'postpack'
streamline the extraction, summarization, and diagnostics of specific monitored nodes after model fitting.
Further, because there is rarely only ever one model under consideration, 'postpack' scales efficiently
to perform the same tasks on output from multiple models simultaneously, facilitating rapid assessment
of model sensitivity to changes in assumptions.

Ben Staton

postpack

Utilities for Processing Posterior Samples Stored in
'mcmc.lists'

density_plot function

<dl><dt>post</dt>
<dd>A <code>mcmc.list</code> object.</dd>
<dt>param</dt>
<dd>A regular expression that matches a single element in the model.
E.g., <code>"b0[1]"</code>, not <code>"b0"</code>. See <code>match_params()</code>.</dd>
<dt>show_diags</dt>
<dd>Control when to display numerical diagnostic summaries on plots. Must be one of
<code>"always"</code>, <code>"never"</code>, or <code>"if_poor_Rhat"</code>. <code>"if_poor_Rhat"</code> (the default)
will display the Rhat and effective MCMC samples if the Rhat statistic
is greater than 1.1.</dd></dl>

Arguments

Create a density plot for a single desired node — density_plot

<dl>

<dt>post</dt>
<dd>A <code>mcmc.list</code> object.</dd>


<dt>param</dt>
<dd>A regular expression that matches a single element in the model.
E.g., <code>"b0[1]"</code>, not <code>"b0"</code>. See <code>match_params()</code>.</dd>


<dt>show_diags</dt>
<dd>Control when to display numerical diagnostic summaries on plots. Must be one of
<code>"always"</code>, <code>"never"</code>, or <code>"if_poor_Rhat"</code>. <code>"if_poor_Rhat"</code> (the default)
will display the Rhat and effective MCMC samples if the Rhat statistic
is greater than 1.1.</dd>

</dl>

density_plot: Create a density plot for a single desired node

Description

Usage

Value

Arguments