phytools (version 0.1-9)

make.era.map: 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.

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.

References

Paradis, E., J. Claude, and K. Strimmer. 2004. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289--290.

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")