RPANDA (version 1.9)

getDataLikelihood: Likelihood of tip trait values.

Description

Computes -log( likelihood ) of tip trait data under a given set of parameters, and for a specified model of trait evolution.

Usage

getDataLikelihood(object, data, params, v)

Arguments

object

an object of class 'PhenotypicModel'.

data

vector of tip trait data.

params

vector of parameters, given in the same order as in the 'model' object.

v

boolean specifying the verbose mode. Default value : FALSE.

Value

A numerical value : -log( likelihood ) of the model.

References

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

Examples

# NOT RUN {
#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')

#Simulating tip traits under the model :
dataBM <- simulateTipData(modelBM, c(0,0,0,1))

#Likelihood of the data :
getDataLikelihood(modelBM, dataBM, c(0,0,0,1))
# }