foreground2Tree: Creates a tree from a set of foreground species

Description Usage Arguments Value

View source: R/RERfuncs.R

Description

Creates a tree from a set of foreground species

Usage

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foreground2Tree(foreground, treesObj, collapse2anc = T, plotTree = T,
  wholeClade = F, clade = c("ancestral", "terminal", "all",
  "weighted"))

Arguments

treesObj

A treesObj created by readTrees

collapse2anc

Put all the weight on the ancestral branch when the trait appears on a whole clade (redundant to "clade", kept for backwards compatibility)

plotTree

Plot a tree representation of the result

wholeClade

Whether to implement the weighted edge option across all members of a foreground clade (redundant to "clade", kept for backwards compatibility)

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".

foreground.

A character vector containing the foreground species

Value

A tree with edge.lengths representing phenotypic states


nclark-lab/RERconverge documentation built on Aug. 15, 2018, 4:38 a.m.