read.RevBayes

Features tools for exploring congruent phylogenetic birth-death models. It can construct the pulled speciation- and net-diversification rates from a reference model. Given alternative speciation- or extinction rates, it can construct new models that are congruent with the reference model. Functionality is included to sample new rate functions, and to visualize the distribution of one congruence class. See also Louca & Pennell (2020) <doi:10.1038/s41586-020-2176-1>.

Bjørn Tore Kopperud

CRABS

Congruent Rate Analyses in Birth-Death Scenarios

Sebastian Höhna

Andrew F. Magee

Jérémy Andréoletti

read.RevBayes function

<dl><dt>x</dt>
<dd>path to log, or data frame</dd>
<dt>n_times</dt>
<dd>number of time knots</dd>
<dt>max_t</dt>
<dd>tree height</dd>
<dt>n_samples</dt>
<dd>first n posterior samples</dd>
<dt>summary_type</dt>
<dd>either "none" for all the posterior samples, or "mean" or "median" for the posterior mean/median</dd>
<dt>extinction_prefix</dt>
<dd>the prefix string for the extinction rate column names. Must be unique</dd>
<dt>speciation_prefix</dt>
<dd>the prefix string for the speciation rate column names. Must be unique</dd></dl>

Arguments

read RevBayes log file — read.RevBayes

<dl>

<dt>x</dt>
<dd>path to log, or data frame</dd>


<dt>n_times</dt>
<dd>number of time knots</dd>


<dt>max_t</dt>
<dd>tree height</dd>


<dt>n_samples</dt>
<dd>first n posterior samples</dd>


<dt>summary_type</dt>
<dd>either "none" for all the posterior samples, or "mean" or "median" for the posterior mean/median</dd>


<dt>extinction_prefix</dt>
<dd>the prefix string for the extinction rate column names. Must be unique</dd>


<dt>speciation_prefix</dt>
<dd>the prefix string for the speciation rate column names. Must be unique</dd>

</dl>

read.RevBayes: read RevBayes log file

Description

Usage

Value

Arguments

Examples