# NOT RUN {
## 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 one 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.
ML.RatePhylo(anolis.rateData, fixed=c(1, FALSE, FALSE, FALSE), pretty=TRUE, lambda.est = FALSE)
# }
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