phyloMean: Calculation of phylogenetically corrected mean.

In PuttickMacroevolution/motmot.2.0: Models of Trait Macroevolution on Trees

Description

This function calculates the phylogenetic mean of the data given the tree and model of evolution

Usage

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

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	Numeric value for lambda from 0-1.
meserr	Logical. Include measurement error.

Value

mu phylogenetically corrected mean

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

 ## 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. 

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

PuttickMacroevolution/motmot.2.0 documentation built on June 11, 2020, 10:51 p.m.