parse.slide.clades

Converts a list of clades (e.g., "1 2 3 4" as a clade) and
returns a list of parsed clades, converting numbers to names using a set of trees.
Called internally by the slide and cumulative analyses, not user-facing.

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

parse.slide.clades function

<dl><dt>clades</dt>
<dd>A list of clades, as in the first column of a cladetable in an rwty.slide or rwty.cumulative object.</dd>
<dt>treelist</dt>
<dd>A list of trees, used for getting tip names.</dd></dl>

Arguments

Rename clades for easy recall — parse.slide.clades

<dl>

<dt>clades</dt>
<dd>A list of clades, as in the first column of a cladetable in an rwty.slide or rwty.cumulative object.</dd>


<dt>treelist</dt>
<dd>A list of trees, used for getting tip names.</dd>

</dl>

Rename clades for easy recall

parse.slide.clades: Rename clades for easy recall

Description

Usage

Value

Arguments