treeTrans: treeTrans

In hferg/btrtools:

Description

A function that transforms a tree, or a local part of a tree, according to lambda, kappa, delta, or a local rate.

Usage

treeTrans(tree, param, nodes = "root", tips = NULL, value,
  rescale = FALSE)

Arguments

tree	A tree of class phylo
param	The transformation applied to the tree, either "lambda", "kappa", "delta", "rate" or "EB".
nodes	A node number or vector of nodes describing the clade(s) to be transformed.
tips	A vector, or list of vectors, of tip labels definining clade(s) to be transformed
value	The value or vector of values to apply to the tree or parts of the tree. Order corresponds to the order of the elements of nodes or tips.
rescale	Whether or not to rescale the tree to have the same root-to-tip length after transformation. Defaults to TRUE.

Examples

transTree(tree, param = "lambda", nodes = 52, value = 0)
transTree(tree, param = "rate", nodes = c(52, 91), value = 3)
transTree(tree, param = "delta", tips = list(c("dog", "cat", "moose"), c("frog", "salamander", "newt")), value = c(0.3, 2))

hferg/btrtools documentation built on May 17, 2019, 3:56 p.m.