as.rateMatrix: Conversion among data and phylogeny objects

In PuttickMacroevolution/motmot: Models of Trait Macroevolution on Trees

Description

Function to generate a rateMatrix object containing a set of variance covariance matrices. Note that as.rateMatrix calls the CAIC function vcv.array multiple times and this can be slow for large phylogenies (though faster than using the ape equivalent vcv.phylo).

Usage

as.rateMatrix(phy, x, data)

Arguments

phy	An object of class "phylo" (see ape).
x	The explanatory (discrete) variable used to define the hypothesised rate categories. Can be specified as a column number or column name
data	The explanatory (discrete) variable used to define the hypothesised rate categories. Can be specified as a column number or column name

Value

rateMatrix An object of class "rateMatrix" - a list of matrices describing the expected variances and covariances of between species. Each matrix refers to the variances and covariances for a given state of x (see Thomas et al. 2006).

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.

Examples

## Read in phylogeny and data from Thomas et al. (2009)
data(anolis.tree)
data(anolis.data)

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

PuttickMacroevolution/motmot documentation built on June 5, 2020, 7 p.m.