convevol (version 1.0)

convrat: Quantify convergence by the ratio of the current to maximum past phenotypic distance

Description

convrat quantifies convergence in a number of different ways. The basic method uses 1-(dtip/dmax) or dmax/dtip, where dtip is the current phenotypic distance between taxa and dmax is the maximum phenotypic distance between the ancestors of those taxa. This function also scales this measure in a variety of ways.

Usage

convrat(phyl, phendata, convtips)

Arguments

phyl

The phylogeny of interest in phylo format

phendata

Phenotypic data for all tips

convtips

A list consisting of the names of all convergent taxa

Value

C1, C2, C3, and C4

Details

C1 = 1-(dtip/dmax). C2 = dmax-dtip. C3 is C2 scaled by the total amount of evolution that has occured in the clade descendend from the most recent common ancestor of all convergent tips. C4 is C2 scaled by the total amount of evolution in the phylogeny. This program assumes that all monophyletic clades composed entirely of putatively convergent taxa have been reduced to averages or representative taxa.

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=2)
convtips<-c("t1","t2","t3")
answer<-convrat(phyl,phendata,convtips)
# }