likRatePhylo {motmot}

Log-likelihood rate estimation for traits and phylogenies

Description

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

Usage

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

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

Logical. Numeric value for lambda from 0-1.

meserr

Logical. Logical. Include measurement error.

sigmaScale

Logical. Scalar for measurement error relative to tree.

Value

ll log-likelihood of the model

mu phylogenetically corrected mean(s)

s2 Brownian variance

Note

The means are output as treatment contrasts.

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

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 

# 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)