get_traces

This function takes the provided <code>libbi</code> object
 which has been run and returns a data frame with the parameter
 traces.

Provides a complete interface to 'LibBi', a library for Bayesian
inference (see <https://libbi.org> and Murray, 2015
<doi:10.18637/jss.v067.i10> for more information). This includes functions
for manipulating 'LibBi' models, for reading and writing 'LibBi'
input/output files, for converting 'LibBi' output to provide traces for use
with the coda package, and for running 'LibBi' to conduct inference.

Sebastian Funk

Interface to 'LibBi'

Pierre E. Jacob

Anthony Lee

Lawrence M. Murray

Sam Abbott

get_traces function

<dl><dt>x</dt>
<dd>a <code>libbi</code> object which has been run, or a
list of data frames containing parameter traces (as returned by
<code>bi_read</code>); if it is not a <code>libbi</code>
object, either 'all' must be TRUE or a model given</dd>
<dt>model</dt>
<dd>a model to get the parameter names from; not needed if
'run' is given as a <code>libbi</code> object or 'all' is set
to TRUE</dd>
<dt>burnin</dt>
<dd>proportion of iterations to discard as burn-in (if between 0
and 1), or number of samples to discard (if &gt;1)</dd>
<dt>all</dt>
<dd>whether all variables in the run file should be
considered (otherwise, just parameters)</dd>
<dt>...</dt>
<dd>parameters to <code>bi_read</code> (e.g., dimensions)</dd></dl>

Arguments

Get the parameter traces — get_traces

<dl>

<dt>x</dt>
<dd>a <code>libbi</code> object which has been run, or a
list of data frames containing parameter traces (as returned by
<code>bi_read</code>); if it is not a <code>libbi</code>
object, either 'all' must be TRUE or a model given</dd>


<dt>model</dt>
<dd>a model to get the parameter names from; not needed if
'run' is given as a <code>libbi</code> object or 'all' is set
to TRUE</dd>


<dt>burnin</dt>
<dd>proportion of iterations to discard as burn-in (if between 0
and 1), or number of samples to discard (if &gt;1)</dd>


<dt>all</dt>
<dd>whether all variables in the run file should be
considered (otherwise, just parameters)</dd>


<dt>...</dt>
<dd>parameters to <code>bi_read</code> (e.g., dimensions)</dd>

</dl>

get_traces: Get the parameter traces

Description

Usage

Value

Arguments