# ratematrix: evolutionary VCV matrix In geiger: Analysis of Evolutionary Diversification

 ratematrix R Documentation

## 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 `n`x`n` matrix. Diagonal elements represent rate estimates for individual characters, while off-diagonal elements represent the estimated covariance between two characters.

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)

``````

geiger documentation built on April 4, 2023, 1:07 a.m.