foreground2Tree: Creates a binary trait tree from a set of foreground species.

Description Usage Arguments Value

View source: R/RERfuncs.R

Description

Creates a binary trait 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"), useSpecies = NULL)

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".

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 tree with edge.lengths representing phenotypic states


nclark-lab/RERconverge documentation built on Dec. 3, 2018, 7:12 p.m.