phyloVar: Calculation of Brownian variance. In motmot.2.0: Models of Trait Macroevolution on Trees

Description

This function calculates the phylogenetic variance (Brownian variance, or rate) of the data given the tree and model of evolution

Usage

 1 2 phyloVar(rateData, rate = NULL, common.mean = FALSE, lambda.est = TRUE, lambda = 1, meserr = FALSE)

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. common.mean a logical specififying whether each rate category should have its own mean (common.mean=FALSE) or all categories should have the same mean (common.mean=FALSE). See Thomas et al. (2009) for a discussion on the impact of assumptions about mean on rate estimates. lambda.est Logical. Fit Pagel's lambda. lambda Numeric value for lambda from 0-1. meserr Logical. Include measurement error.

Value

phylo.var phylogenetic variance (Brownian variance)

Author(s)

Gavin Thomas, Rob Freckleton

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

 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 ## Read in phylogeny and data from Thomas et al. (2009) 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) # A model with a different rate in each of the four groups. The 'fixed' command is used to determine # whether a particular rate is to be constrained or not. Use '1' to fix a group and 'FALSE' to show # that the parameter is not fixed and should be estimated. The values should be entered in the same # order as the ranking of the groups. That is, group 0 (small islands) takes position one in the # fixed vector, group 1 (large island trunk crown and trunk ground) takes position 2 and so on. # The default is to allow each group to take a different mean. phyloVar(anolis.rateData, rate=c(1,2,1,1), common.mean=FALSE) # common mean for all groups phyloVar(anolis.rateData, rate=c(1,2,1,1), common.mean=TRUE)

motmot.2.0 documentation built on May 1, 2019, 9:22 p.m.