geiger (version 1.0-91)

ape2ouch: Convert between ape and ouch formats

Description

Converts phylogenetic trees between ape 'phylo' format (used by geiger, ape, and laser packages) and ouch format (used by the ouch package). The OUCH package can be used for testing the Ornstein-Uhlenbeck model of evolution, among other things. If the tree and data file have taxa that don't match, they will be removed from the analysis.

Usage

ape2ouch(phy, data, data.names=NULL)

Arguments

phy

An object of class phylo

data

Data vector

data.names

Tip names for data vector that match tree species; ignored if data includes names

Value

• ape2ouch returns the phylogentic tree in ouch format as a list with the following components:
• d
  Phenotypic values in ouch format
• node
  Node list for a phylogenetic tree, ouch format
• ancestor
  Ancestor list for a phylogenetic tree, ouch format
• time
  Branch times for a phylogenetic tree, ouch format
• species
  Species names for a phylogenetic tree, ouch format

References

Butler, M.A. and A.A. King, 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164:683-695.

Examples

data(geospiza)
attach(geospiza)

ape2ouch(geospiza.tree, geospiza.data[,1], rownames(geospiza.data))->geospiza.ouch

#Interface with ouch package
library(ouch)

brown.fit(geospiza.ouch$d, geospiza.ouch$node, geospiza.ouch$ancestor, geospiza.ouch$time)