make.likRatePhylo: Internal function

In motmot: Models of Trait Macroevolution on Trees

Description

Internal function. Constructor to allow fixing of rate parameters.

Usage

make.likRatePhylo(rateData, fixed, common.mean = FALSE, lambda.est, meserr)

Arguments

rateData	an object of class "rateData"
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).
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 - Logical. Fit Pagel's lambda.
meserr	an object of class "rateData"

Value

Returns a function to be passed to optim.likRatePhylo

Author(s)

Gavin Thomas

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