generate_dataset

This is a wrapper around <code>libbi sample --target joint
 --nsamples 1</code>, to generate a synthetic dataset from a model. Parameters can
 be passed via the 'init' option (see <code>run.libbi</code>, otherwise
 they are generated from the prior specified in the model. The end time
 should be specified using the "end_time" option. If this is not given, only
 a parameter set is sampled. Use the 'noutputs' or 'output_every' options to
 control the number of data points being generated. By default, output_every
 is set to 1.

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

generate_dataset function

<dl><dt>...</dt>
<dd>arguments to be passed to <code>sample.libbi</code>, especially
'model', 'end_time' and 'seed'.</dd>
<dt>output_every</dt>
<dd>real; if given, <code>noutputs</code> will be set so that there
is output every <code>output_every</code> time steps; if set to 0, only generate
an output at the final time</dd></dl>

Arguments

Generate Dataset — generate_dataset

<dl>

<dt>...</dt>
<dd>arguments to be passed to <code>sample.libbi</code>, especially
'model', 'end_time' and 'seed'.</dd>


<dt>output_every</dt>
<dd>real; if given, <code>noutputs</code> will be set so that there
is output every <code>output_every</code> time steps; if set to 0, only generate
an output at the final time</dd>

</dl>

generate_dataset: Generate Dataset

Description

Usage

Value

Arguments