convevol (version 1.0)

calcchanges: Calculates all phenotypic changes that occur on all branches of a phylogeny.

Description

Calculates the Euclidean distance between all ancestors and descendants on a phylogeny to reconstruct the phenotypic changes that occur along all edges of a phylogeny.

Usage

calcchanges(phyl, phendata)

Arguments

phyl

The phylogeny of interest in phylo format

phendata

A matrix of phenotypic data for all tips, with taxa in rows and characters in columns.

Value

A vector in which each element represents an edge of the phylogeny, and the values are the magnitudes of evolutionary change that occur along those edges.

import ape geiger phytools

Details

Calculates the Euclidean distance between all ancestors and descendants on a phylogeny to reconstruct the phenotypic changes that occur along all edges of a phylogeny.

References

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

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

Examples

# NOT RUN {
phyl<-rtree(10)
phendata<-fastBM(phyl,nsim=5)
changes<-calcchanges(phyl,phendata)
# }