phyloVar: Calculation of Brownian variance.

In motmot: 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

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

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.

motmot documentation built on May 2, 2019, 4:48 p.m.