phyloVar: Calculation of Brownian variance.
In PuttickMacroevolution/motmot: Models of Trait Macroevolution on Trees

Description Usage Arguments Value Author(s) References Examples

This function calculates the phylogenetic variance (Brownian variance, or rate) of the data given the tree and model of evolution

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

`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.

phylo.var phylogenetic variance (Brownian variance)

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. @references Thomas GH, Meiri S, & Phillimore AB. 2009. Body size diversification in Anolis: novel environments and island effects. Evolution 63, 2017-2030.

 ## Read in phylogeny and data from Thomas et al. (2009)
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)

# A model with a different rate in each of the four groups. The 'fixed' command is used to determine
# whether a particular rate is to be constrained or not. Use '1' to fix a group and 'FALSE' to show
# that the parameter is not fixed and should be estimated. The values should be entered in the same 
# order as the ranking of the groups. That is, group 0 (small islands) takes position one in the 
# fixed vector, group 1 (large island trunk crown and trunk ground) takes position 2 and so on. 
# The default is to allow each group to take a different mean. 

phyloVar(anolis.rateData, rate=c(1,2,1,1), common.mean=FALSE)
# common mean for all groups
phyloVar(anolis.rateData, rate=c(1,2,1,1), common.mean=TRUE)