optim.likRatePhylo: Maximum likelihood rate estimation for traits and phylogenies

In ghthomas/motmot: Models of Trait Macroevolution on Trees

Description

Function for the maximum likelihood estimation of rate parameters on a trait and phylogeny.

Usage

optim.likRatePhylo(rateData, rate = NULL, fixed = NULL, rateMIN = 0.001, rateMAX = 50, common.mean = FALSE, lambda.est=TRUE, 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.
fixed	A vector stating whether each parameter should be allowed to vary (either FALSE which results in a start value of 1, or a numeric start value) or should be fixed (TRUE).
rateMIN	Minimum value for the rate parameters
rateMAX	Maximum value for the rate parameters
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.
meserr	Logical. Include measurement error.

Value

MLRate	Maximum likelihood estimates of the rate parameters
Max.lik	Maximum (log) likeihood
AIC	AIC for maximum likelihood model
AICc	AICc for maximum likelihood model
convergence	convergence value from optim
n.parameters	Number of parameters in the model (how many means and rate categories)

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.

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