geiger (version 0.2-6)

ape2ouch: Convert between ape and ouch formats

Description

Converts phylogenetic trees between ape format (used by geiger, ape, and laser packages) and ouch format (used by the ouch package)

Usage

ape2ouch(phy, data)

Arguments

phy

Phylogenetic tree in ape format

data

Data vector with names that match tip species

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

Geiger2

Examples

data(geospiza)
attach(geospiza)
name.check(geospiza.data, geospiza.tree)->r
drop.tip(geospiza.tree, r[[1]])->g.tree

data<-geospiza.data[,1]
names(data)<-rownames(geospiza.data)

ape2ouch(g.tree, data)->geospiza.ouch

#Interface with ouch package
library(ouch)

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