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

Description Usage Arguments Value Author(s) References See Also Examples

Simulates trait data on a tree using a specified model of evolution (see details).

transformPhylo.sim(
  phy,
  n = 1,
  x = NULL,
  model = NULL,
  returnNodes = FALSE,
  kappa = NULL,
  lambda = NULL,
  delta = NULL,
  alpha = NULL,
  psi = NULL,
  acdcRate = NULL,
  lambda.sp = NULL,
  trend = NULL,
  trend.anc.state = 0,
  nodeIDs = NULL,
  rateType = NULL,
  cladeRates = NULL,
  branchRates = NULL,
  rate = NULL,
  group.means = NULL,
  splitTime = NULL,
  timeRates = NULL,
  branchLabels = NULL,
  rate.var = NULL,
  mode.order = NULL
)

`phy`	An object of class `phylo` (see ape).
`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).
`returnNodes`	Logical. If TRUE, alongside the tip values all node values are returned corresponding to APE's edge.matrix for the tree.
`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
`trend`	value of the expectation mean change through time
`trend.anc.state`	the expected ancestal state for the trend model (default is 0)
`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 or logical to indicate scalar is included in the 'modeslice' model (the scalar is included in the mode.param argument with the 'modeslice' model).
`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.
`rate.var`	Allows rate variation in BM modes in the 'modeslice' model
`mode.order`	The order of modes for the 'modeslice' model. Any combination of 'BM', 'OU', 'acdc', and 'kappa'

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

transformPhylo.ML, transformPhylo.ll, transformPhylo, transformPhylo.MCMC

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))