simulateTipData: Tip trait simulation under a model of phenotypic evolution.

In RPANDA: Phylogenetic ANalyses of DiversificAtion

Tip trait simulation under a model of phenotypic evolution.

Description

Simulates tip trait data under a specified model of phenotypic evolution, with three distinct behaviours specified with the 'method' argument.

Usage

simulateTipData(object, params, method, v)

Arguments

object	an object of class 'PhenotypicModel'.
params	vector of parameters, given in the same order as in the 'model' object.
method	an integer specifying the behaviour of the function. If method = 1 (default value), the tip distribution is first computed, before returning a simulated dataset drawn in this distribution. If method = 2, the whole trajectory is simulated step by step, plotted, and returned. Otherwise, the whole trajectory is simulated step by step, and then returned without being plotted.
v	boolean specifying the verbose mode. Default value : FALSE.

Value

a vector of trait values at the tips of the tree.

Author(s)

M Manceau

References

Manceau M., Lambert A., Morlon H. (2017) A unifying comparative phylogenetic framework including traits coevolving across interacting lineages Systematic Biology

Examples

#Loading an example tree
newick <- "((((A:1,B:0.5):2,(C:3,D:2.5):1):6,E:10.25):2,(F:6.5,G:8.25):3):1;"
tree <- read.tree(text=newick)

#Creating the models
modelBM <- createModel(tree, 'BM')
modelOU <- createModel(tree, 'OU')

#Simulating tip traits under both models with distinct behaviours of the functions :
dataBM <- simulateTipData(modelBM, c(0,0,0,1))
dataOU <- simulateTipData(modelOU, c(0,0,1,5,1), method=1)
dataBM2 <- simulateTipData(modelBM, c(0,0,0,1), method=2)

RPANDA documentation built on Oct. 24, 2022, 5:06 p.m.