transformRateMatrix: Conversion among data and phylogeny objects

In ghthomas/motmot: Models of Trait Macroevolution on Trees

Description

Transforms the expected variance and covariances among species according to hypotheses of rate variation between lineages.

Usage

transformRateMatrix(rateData, rate = NULL)

Arguments

rateData	an object of class "rateData"
rate	a vector of relative rate parameters. The length of the vector is equal to the number of rates being estimated. If rate=NULL then rates are equal.

Value

retMat

Rate-transformed variance covariance matrix

Author(s)

Gavin Thomas

References

Thomas GH, Freckleton RP, & Szekely T. 2006. Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds. Proceedings of the Royal Society B 273, 1619-1624.

Thomas GH, Meiri S, & Phillimore AB. 2009. Body size diversification in Anolis: novel environments and island effects. Evolution 63, 2017-2030.

Examples

data(anolis.tree)
data(anolis.data)

## Convert data to class rateData with a rateMatrix object as input
anolis.rateMatrix <- as.rateMatrix(phy=anolis.tree, x="geo_ecomorph", data=anolis.data)

anolis.rateData <- as.rateData(y="Female_SVL", x="geo_ecomorph", 
rateMatrix = anolis.rateMatrix, phy=NULL, data=anolis.data, log.y=TRUE)

# Tranform the expected variance covariance matrix so that the rates in the first and last 
# categories are equal (both 1) whereas the rate in the second category is twice as fast (2) and 
# the rate in the third category is ten times slower.

trans.anolis.rateData <- transformRateMatrix(rateData=anolis.rateData, rate = c(1,2,0.1,1))

ghthomas/motmot documentation built on July 31, 2018, 12:11 a.m.