foreground2Paths: Creates paths from a set of foreground species

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

Creates paths from a set of foreground species

Description

Creates paths from a set of foreground species

Usage

foreground2Paths(
  foreground,
  treesObj,
  plotTree = F,
  clade = c("ancestral", "terminal", "all", "weighted"),
  useSpecies = NULL
)

Arguments

treesObj	A treesObj created by readTrees
plotTree	Plot a tree representation of the result
clade	A character string indicating which branches within the clade containing the foreground species should be set to foreground. Must be one of the strings "ancestral", "terminal", "all", or "weighted".
useSpecies	Give only a subset of the species to use for ancestral state reconstruction (e.g., only those species for which the trait can be reliably determined).
foreground.	A character vector containing the foreground species

Value

A vector of length equal to the number of paths in treesObj

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