load.multi

Finds trees and log files based on format definition, returns rwty.chain objects containing both

phylogenetics

MCMC

Trees

load

Implements various tests, visualizations, and metrics
for diagnosing convergence of MCMC chains in phylogenetics. It implements
and automates many of the functions of the AWTY package in the R
environment, as well as a host of other functions. Warren, Geneva, and Lanfear (2017), <doi:10.1093/molbev/msw279>.

Dan Warren

rwty

R We There Yet? Visualizing MCMC Convergence in Phylogenetics

Anthony Geneva

Rob Lanfear

Luke Harmon

April Wright

Diego Mallo

Klaus Schliep

Kelly Luke

Kendall Michelle

Smith Martin

load.multi function

<dl><dt>path</dt>
<dd>The path to the directory containing tree and log files</dd>
<dt>format</dt>
<dd>File format, which is used to find tree and log files.
Currently accepted values are "mb" for MrBayes, "beast" for BEAST, "*beast" for *BEAST, and "revbayes" for RevBayes.
If you would like RWTY to understand additional formats, please contact the authors and send us some sample data.</dd>
<dt>labels</dt>
<dd>A vector of names to assign to chains as they are read in.</dd>
<dt>...</dt>
<dd>Further arguments to be passed to load.trees.</dd></dl>

Arguments

Load all matching files from a directory into a list of rwty.chain objects — load.multi

<dl>

<dt>path</dt>
<dd>The path to the directory containing tree and log files</dd>


<dt>format</dt>
<dd>File format, which is used to find tree and log files.
Currently accepted values are "mb" for MrBayes, "beast" for BEAST, "*beast" for *BEAST, and "revbayes" for RevBayes.
If you would like RWTY to understand additional formats, please contact the authors and send us some sample data.</dd>


<dt>labels</dt>
<dd>A vector of names to assign to chains as they are read in.</dd>


<dt>...</dt>
<dd>Further arguments to be passed to load.trees.</dd>

</dl>

Load all matching files from a directory into a list of rwty.chain objects

load.multi: Load all matching files from a directory into a list of rwty.chain objects

Description

Usage

Value

Arguments

Examples