convevol (version 1.0)

allmaxdist: Calculates maxdist for all pairs of taxa in a phylogeny.

Description

allmaxdist Uses maxdist to calcualte the maximum phenotypic. distance between the ancestors of all pairs of taxa in a phylogeny. By default outputs these as a matrix, but can also output a list. Can take some time to run for large trees.

Usage

allmaxdist(phyl, phendata, mat = TRUE)

Arguments

phyl

The phylogeny of interest in phylo format

phendata

Phenotypic data for all tips

mat

Whether or not to export the values in a matrix (default) or a list

Value

A matrix or list of all maxdist values for all pairs of taxa in the phylogeny.

Details

Regarding the output: the matrix is better organized, but the list avoids all the zeroes and is probably better for making histograms.

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)
answer<-allmaxdist(phyl,phendata,mat=TRUE)
# }