simBinPheno: Generates a permulated phylogenetic tree with specified...

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

Generates a permulated phylogenetic tree with specified number of foreground branches. User may specify the number of foreground branches that are internal branches.

Description

Generates a permulated phylogenetic tree with specified number of foreground branches. User may specify the number of foreground branches that are internal branches.

Usage

simBinPheno(trees, root, phenvec, fgnum = NULL, internal = 0, drop = NULL)

Arguments

trees	treesObj output from readTrees
root	Species on which to root the master tree
phenvec	Named vector of 1's and 0's representing phenotype values for each species
fgnum	Total number of foreground species - only required if internal foreground branches are required
internal	Number of foreground species that should be internal branches - only required if internal foreground branches are required
drop	Character vector (or single character variable) of species names to be removed from the master tree (such as species in trees but not in phenotype vector)

Value

A tree with permulated phenotype values

nclark-lab/RERconverge documentation built on March 2, 2024, 8:51 a.m.