transformPhylo.sim: Phylogenetic tree transformations
In motmot.2.0: Models of Trait Macroevolution on Trees

Description Usage Arguments Value Author(s) References Examples

Transforms the branch lengths of a phylo object according to a model of trait evolution (see details).

transformPhylo.sim(phy, n = 1, x = NULL, model = NULL, kappa = NULL,
  lambda = NULL, delta = NULL, alpha = NULL, psi = NULL,
  acdcRate = NULL, lambda.sp = NULL, nodeIDs = NULL, rateType = NULL,
  cladeRates = NULL, branchRates = NULL, rate = NULL,
  group.means = NULL, splitTime = NULL, timeRates = NULL,
  branchLabels = NULL)

`phy`	An object of class "phylo" (see ape package).
`n`	Number of simulations
`x`	Vector, matrix or data.frame (with taxon names as names or rownames) of categories for each species. Only applicable if model="mixedRate"
`model`	The model of trait evolution (see details).
`kappa`	Value of kappa transform.
`lambda`	Value of lambda transform.
`delta`	Value of delta transform.
`alpha`	Value of alpha (OU) transform.
`psi`	Value of psi transform. Note that 'original nodes' from the full phylogeny can be included as an element on the phylogeny (e.g., phy$orig.node) as well as estimates of 'hidden' speciation (e.g., phy$hidden.speciation) if estimates of extinction (mu) are > 0.
`acdcRate`	Value of ACDC transform.
`lambda.sp`	Estimate of speciation (lambda) for the psi models
`nodeIDs`	Integer - ancestral nodes of clades.
`rateType`	If model="clade", a vector specifying if rate shift occurs in a clade ("clade") or on the single branch leading to a clade ("branch").
`cladeRates`	Numeric vector specifying telative rates for clades.
`branchRates`	Numeric vector specifying relative rates for individual branches
`rate`	a vector of relative rate parameters. The length of the vector is equal to the number of rates being estimated.
`group.means`	a vector of the relative difference in means between rate categories, expressed as a scalar applied to the expected standard deviation (see Ricklefs 2006)
`splitTime`	A split time (measured from the present, or most recent species) at which a shift in the rate occurs for the "timeSlice" model
`timeRates`	The rates (from ancient to recent) for the timeSlice model
`branchLabels`	Branches on which different psi parameters are estimated in the "multipsi" model.

Returns a matrix of simulated dated with taxon names as rownames (number of columns=n).

Gavin Thomas, Mark Puttick

Ricklefs RE. 2006. Time, species, and the generation of trait variation in clades. Systematic Biology 55, 151-159.

Ricklefs RE. 2006. 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)

# Simulate 10 sets of data with kappa=0.1 using the anolis tree
sim.dat1 <- transformPhylo.sim(phy=anolis.tree, n=10, model="kappa", kappa=0.1)

# Simulate 10 sets of data where rates and means differ between to the categories defined by "x"
x <- anolis.data$geo_ecomorph
names(x) <-  rownames(anolis.data)
sim.dat2 <- transformPhylo.sim(phy=anolis.tree, n=10, x=x, model="mixedRate", rate=c(1,1,2,4),
group.means=c(0,5,0,0))