mrca_prior_to_xml_taxonset

Creates the <code>taxonset</code> section in the prior section of the
distribution section of a BEAST2 XML parameter file.

'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAUti 2' (which is part of 'BEAST2') is a GUI tool
that allows users to specify the many possible setups
and generates the XML file 'BEAST2' needs to run.
This package provides a way to create 'BEAST2' input
files without active user input, but using
R function calls instead.

Richèl J.C. Bilderbeek

beautier

'BEAUti' from R

Joëlle Barido-Sottani

David Winter

Paul Van Els

Raphael Scherrer

Yacine B. Chehida

Katharine S. Walter

Gary Napier

Jason Griffiths

Thijs Janzen

Pedro Taucce

Olivier Roy

Jana Riederer

mrca_prior_to_xml_taxonset function

<dl><dt>mrca_prior</dt>
<dd>a Most Recent Common Ancestor prior,
as returned by <code>create_mrca_prior</code></dd>
<dt>taxa_names_with_ids</dt>
<dd>taxa names that already have received
an ID. Causes the XML to <code>idref</code> these</dd></dl>

Arguments

Author

Creates the taxonset section in the prior section of the
distribution section of a BEAST2 XML parameter file. — mrca_prior_to_xml_taxonset

<dl>

<dt>mrca_prior</dt>
<dd>a Most Recent Common Ancestor prior,
as returned by <code>create_mrca_prior</code></dd>


<dt>taxa_names_with_ids</dt>
<dd>taxa names that already have received
an ID. Causes the XML to <code>idref</code> these</dd>

</dl>

Creates the <code>taxonset</code> section in the prior section of the
distribution section of a BEAST2 XML parameter file.

mrca_prior_to_xml_taxonset: Creates the `taxonset` section in the prior section of the distribution section of a BEAST2 XML parameter file.

Description

Usage

Value

Arguments

Author

Details