read_Simmap_Rev: Reading stochastic character maps file from ReVBayes

In ontophylo: Ontology-Informed Phylogenetic Comparative Analyses

Reading stochastic character maps file from ReVBayes

Description

Imports stochastic character maps file from RevBayes into R.

Usage

read_Simmap_Rev(file, start = 1, end = 1, save = NULL)

Arguments

file	character. Path to the RevBayes file.
start	integer. First tree of the sample to start reading the RevBayes file.
end	integer. Last tree of the sample to finish reading the RevBayes file.
save	character. Name to save output file.

Value

A tree in 'phylip' format.

Author(s)

Sergei Tarasov

Examples

rev_stm <- "Iteration\t1\t2\t3\tsimmap\n
0\t{1,2.0}\t((spp1:{1,4.0:0,4.0},spp2:{1,2.0:0,6.0}):{1,0.5});\n
1\t{1,2.0}\t((spp1:{1,2.0:0,6.0},spp2:{1,3.0:0,5.0}):{1,0.5});\n
3\t{1,2.0}\t((spp1:{1,2.0:0,6.0},spp2:{1,3.0:0,5.0}):{1,0.5});"
stm <- read_Simmap_Rev(textConnection(rev_stm, "r"), start = 0, end = 3, save = NULL)
stm <- phytools::read.simmap(text = stm, format = "phylip")
phytools::plotSimmap(stm[[1]])

ontophylo documentation built on May 29, 2024, 9:57 a.m.