make.era.map {phytools}R Documentation

Create "era" map on a phylogenetic tree

Description

This function creates a temporal map on the tree based on limits provided by the user.

Usage

make.era.map(tree, limits, ...)

Arguments

tree

a phylogenetic tree as an object of class "phylo".

limits

a vector containing the temporal limits, in time since the root node of the tree, for the mappings.

...

optional arguments.

Value

A modified phylogenetic tree of class "phylo" with the following additional elements:

maps

a list of named vectors containing the times spent in each state on each branch, in the order in which they occur.

mapped.edge

a matrix containing the total time spent in each state along each edge of the tree.

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

See Also

make.simmap, read.simmap, plotSimmap

Examples

tree<-pbtree(n=1000,scale=100)
tree<-make.era.map(tree,c(0,25,50,75))
plotSimmap(tree,pts=FALSE,ftype="off")

[Package phytools version 0.4-60 Index]