ratematrix: evolutionary VCV matrix

In mwpennell/geiger-v2: Analysis of Evolutionary Diversification

evolutionary VCV matrix

Description

estimating the evolutionary or phylogenetic variance-covariance matrix

Usage

ratematrix(phy, dat)

Arguments

phy	a phylogenetic tree of class 'phylo'
dat	a named vector or matrix of continuous trait values, associated with species in phy

Details

If given dat for n quantitative variables, this function returns the estimated evolutionary variance-covariance matrix of the variables under a multivariate Brownian motion model. Note that other evolutionary models may be possible if the tree is first transformed (see rescale.phylo and Examples). If you have n characters in your analysis, this will be an nxn matrix. Diagonal elements represent rate estimates for individual characters, while off-diagonal elements represent the estimated covariance between two characters.

Author(s)

LJ Harmon

References

Revell, L. J., L. J. Harmon, R. B. Langerhans, and J. J. Kolbe. 2007. A phylogenetic approach to determining the importance of constraint on phenotypic evolution in the neotropical lizard, Anolis cristatellus. Evolutionary Ecology Research 9: 261-282.

Examples

geo <- get(data(geospiza))

## EVOLUTIONARY VCV
ratematrix(geo$phy, geo$dat)

## EVOLUTIONARY VCV -- assuming speciational model
kphy <- rescale(geo$phy, "kappa", 0)
ratematrix(kphy, geo$dat)
geo <- get(data(geospiza))

## EVOLUTIONARY VCV
ratematrix(geo$phy, geo$dat)

## EVOLUTIONARY VCV -- assuming speciational model
kphy <- rescale(geo$phy, "kappa", 0)
ratematrix(kphy, geo$dat)

mwpennell/geiger-v2 documentation built on Feb. 26, 2023, 1:19 a.m.