getForegroundInfoClades: Generates a binary phenotype tree and foreground clades...

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

Generates a binary phenotype tree and foreground clades information using the list of tip foreground animals, the presence of foreground common ancestors, and their phylogenetic relationships

Description

Generates a binary phenotype tree and foreground clades information using the list of tip foreground animals, the presence of foreground common ancestors, and their phylogenetic relationships

Usage

getForegroundInfoClades(
  fg_vec,
  sisters_list = NULL,
  trees,
  plotTree = T,
  useSpecies = NULL
)

Arguments

fg_vec	A vector containing the tip foreground species
sisters_list	A list containing pairs of "sister species" in the foreground set (put NULL if empty)
trees	treesObj from readTrees
plotTree	A boolean indicator for plotting the output tree (default=FALSE)
useSpecies	An array containing the tip labels in the output tree

Value

output.list A list containing 1) "tree" = a binary phenotype tree corresponding to the input information, 2) "fg.sisters.table" = a table containing all sister species in the foreground set

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