libbi

<code>libbi</code> allows to call <code>LibBi</code>.
Upon creating a new libbi object, the following arguments can be given.
Once the instance is created, <code>LibBi</code> can be run through the
 <code>sample</code>, <code>filter</code>, or
 <code><a href="/link/optimise?package=rbi&version=1.0.0" data-mini-rdoc="rbi::optimise">optimise</a></code>, or <code>rewrite</code> methods. Note that
 <code>libbi</code> objects can be plotted using <code><a href="/link/plot?package=rbi&version=1.0.0" data-mini-rdoc="rbi::plot">plot</a></code> if the
 <code>rbi.helpers</code> package is loaded.

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

libbi function

<dl><dt>model</dt>
<dd>either a character vector giving the path to a model file
(typically ending in ".bi"), or a <code>bi_model</code> object</dd>
<dt>path_to_libbi</dt>
<dd>path to <code>LibBi</code> binary; by default it tries to
locate the <code>libbi</code> binary using the <code>which</code> Unix command, after
having loaded "~/.bashrc" if present; if unsuccessful it tries
"~/PathToBiBin/libbi"; if unsuccessful again it fails.</dd>
<dt>dims</dt>
<dd>any named dimensions, as list of character vectors</dd>
<dt>use_cache</dt>
<dd>logical; whether to use the cache (default: true)</dd>
<dt>...</dt>
<dd>options passed to <code>run.libbi</code></dd></dl>

Arguments

<code>libbi</code> allows to call <code>LibBi</code>.
Upon creating a new libbi object, the following arguments can be given.
Once the instance is created, <code>LibBi</code> can be run through the
 <code>sample</code>, <code>filter</code>, or
 <code><a href='https://rdrr.io/r/stats/optimize.html'>optimise</a></code>, or <code>rewrite</code> methods. Note that
 <code>libbi</code> objects can be plotted using <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code> if the
 <code>rbi.helpers</code> package is loaded.

LibBi Wrapper — libbi

<dl>

<dt>model</dt>
<dd>either a character vector giving the path to a model file
(typically ending in ".bi"), or a <code>bi_model</code> object</dd>


<dt>path_to_libbi</dt>
<dd>path to <code>LibBi</code> binary; by default it tries to
locate the <code>libbi</code> binary using the <code>which</code> Unix command, after
having loaded "~/.bashrc" if present; if unsuccessful it tries
"~/PathToBiBin/libbi"; if unsuccessful again it fails.</dd>


<dt>dims</dt>
<dd>any named dimensions, as list of character vectors</dd>


<dt>use_cache</dt>
<dd>logical; whether to use the cache (default: true)</dd>


<dt>...</dt>
<dd>options passed to <code>run.libbi</code></dd>

</dl>

libbi: LibBi Wrapper

Description

Usage

Value

Arguments

See Also

Examples