ReadMrBayesTrees

ReadMrBayes

MrBayesTrees

Read posterior trees from <a href="https://nbisweden.github.io/MrBayes/">'MrBayes'</a> output files, discarding burn-in
generations.

Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.

Martin R. Smith

TreeTools

Create, Modify and Analyse Phylogenetic Trees

Emmanuel Paradis

Robert Noble

ReadMrBayesTrees function

<dl><dt>filepath</dt>
<dd>character string specifying path to <code>.nex</code> input file used
to initialize the MrBayes analysis,
relative to the R working directory (visible with <code><a href="/link/getwd()?package=TreeTools&version=1.12.0" data-mini-rdoc="TreeTools::getwd()">getwd()</a></code>).</dd>
<dt>n</dt>
<dd>Integer specifying number of trees to sample from posterior.</dd>
<dt>burninFrac</dt>
<dd>Fraction of trees to discard from each run as burn-in.
If <code>NULL</code> (the default), this will be read from the last <code>mcmc</code> or <code>mcmcp</code>
command in <code>filepath</code>.</dd></dl>

Arguments

<a href="https://orcid.org/0000-0001-5660-1727">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=TreeTools&version=1.12.0" data-mini-rdoc="TreeTools::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

Read posterior trees from <a href='https://nbisweden.github.io/MrBayes/'>'MrBayes'</a> output files, discarding burn-in
generations.

Read posterior tree sample produced by MrBayes — ReadMrBayesTrees

<dl>

<dt>filepath</dt>
<dd>character string specifying path to <code>.nex</code> input file used
to initialize the MrBayes analysis,
relative to the R working directory (visible with <code><a href='https://rdrr.io/r/base/getwd.html'>getwd()</a></code>).</dd>


<dt>n</dt>
<dd>Integer specifying number of trees to sample from posterior.</dd>


<dt>burninFrac</dt>
<dd>Fraction of trees to discard from each run as burn-in.
If <code>NULL</code> (the default), this will be read from the last <code>mcmc</code> or <code>mcmcp</code>
command in <code>filepath</code>.</dd>

</dl>

<a href='https://orcid.org/0000-0001-5660-1727'>Martin R. Smith</a>
(<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

ReadMrBayesTrees: Read posterior tree sample produced by MrBayes

Description

Usage

Value

Arguments

Author

Details

See Also

Examples