likRatePhylo: Log-likelihood rate estimation for traits and phylogenies
In ghthomas/motmot: Models of Trait Macroevolution on Trees

Description Usage Arguments Value Note Author(s) References Examples

This function calculates the log-likelihood, phylogenetic mean, and Brownian variance for a trait and a phylogeny transformed according to variation in relative rates.

1	likRatePhylo(rateData, rate = NULL, common.mean = FALSE, lambda.est, lambda, meserr, sigmaScale)

`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.
`sigmaScale`	Scalar for measurement error relative to tree.

`ll`	log-likelihood of the model
`mu`	phylogenetically corrected mean(s)
`s2`	Brownian variance

The means are output as treatment contrasts.

Gavin Thomas, Rob Freckleton

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.

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)

## Calculate phylogenetic mean, variance, log likelihood for a model where the first rate category 
#  (small islands) takes position one in the rate vector, group 1 (large island trunk crown and trunk 
#  ground) takes position 2 and so on. The rates in the first and last categories are equal (both 1) 
#  whereas the rate in the second category is twice as fast (2) and the rate in the third category is 
#  ten times slower. Means are allowed to differ. 

# mean only
phyloMean(rateData=anolis.rateData, rate = c(1,2,0.1,1), common.mean = FALSE)

# variance only
phyloVar(rateData=anolis.rateData, rate = c(1,2,0.1,1), common.mean = FALSE) 

# mean, variance and log-likelihood
likRatePhylo(rateData=anolis.rateData, rate = c(1,2,0.1,1), common.mean = FALSE)