tracedens_jags

Combination of trace plots and by-chain kernel densities of a whole <code>jagsUI</code> object, or optional subset of parameter nodes.

Tools are provided to streamline Bayesian analyses in 'JAGS' using
the 'jagsUI' package. Included are functions for extracting output in
simpler format, functions for streamlining assessment of convergence, and
functions for producing summary plots of output. Also included is a
function that provides a simple template for running 'JAGS' from 'R'.
Referenced materials can be found at <DOI:10.1214/ss/1177011136>.

Matt Tyers

jagshelper

Extracting and Visualizing Output from 'jagsUI'

tracedens_jags function

<dl><dt>x</dt>
<dd>Posterior <code>jagsUI</code> object</dd>
<dt>p</dt>
<dd>Parameter name for subsetting: if this is specified, only parameters with names beginning with this string will be plotted.</dd>
<dt>exact</dt>
<dd>Whether <code>p</code> should be an exact match (<code>TRUE</code>) or just match the
beginning of the string (<code>FALSE</code>). Defaults to <code>FALSE</code>.</dd>
<dt>parmfrow</dt>
<dd>Optional call to <code>par(mfrow)</code> for the number of rows &amp; columns of plot window. Returns the graphics device to previous state afterward.</dd>
<dt>lwd</dt>
<dd>Line width for plotting. Defaults to 1.</dd>
<dt>shade</dt>
<dd>Whether to add semi-transparent shading to by-chain kernel densities. Defaults to <code>TRUE</code>.</dd>
<dt>...</dt>
<dd>additional plotting arguments</dd></dl>

Arguments

Author

Combination of trace plots and by-chain kernel densities of jagsUI object — tracedens_jags

<dl>

<dt>x</dt>
<dd>Posterior <code>jagsUI</code> object</dd>


<dt>p</dt>
<dd>Parameter name for subsetting: if this is specified, only parameters with names beginning with this string will be plotted.</dd>


<dt>exact</dt>
<dd>Whether <code>p</code> should be an exact match (<code>TRUE</code>) or just match the
beginning of the string (<code>FALSE</code>). Defaults to <code>FALSE</code>.</dd>


<dt>parmfrow</dt>
<dd>Optional call to <code>par(mfrow)</code> for the number of rows &amp; columns of plot window. Returns the graphics device to previous state afterward.</dd>


<dt>lwd</dt>
<dd>Line width for plotting. Defaults to 1.</dd>


<dt>shade</dt>
<dd>Whether to add semi-transparent shading to by-chain kernel densities. Defaults to <code>TRUE</code>.</dd>


<dt>...</dt>
<dd>additional plotting arguments</dd>

</dl>

tracedens_jags: Combination of trace plots and by-chain kernel densities of `jagsUI` object

Description

Usage

Value

Arguments

Author

See Also

Examples