simBinPhenoSSM: Produces one SSM binary permulation for a gene

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

Produces one SSM binary permulation for a gene

Description

Produces one SSM binary permulation for a gene

Usage

simBinPhenoSSM(
  tree,
  trees,
  root_sp,
  fg_vec,
  sisters_list = NULL,
  pathvec,
  plotTreeBool = F
)

Arguments

tree	Tree of the gene of interest
trees	treesObj from readTrees
root_sp	The species to root the tree on
fg_vec	A vector containing the foreground species
sisters_list	A list containing pairs of "sister species" in the foreground set (put NULL if empty)
pathvec	A path vector generated from the real set of foreground animals
plotTreeBool	Boolean indicator for plotting the output tree (default=FALSE)

Value

A SSM binary permulated tree

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