createModelCoevolution: Creation of a PhenotypicGMM

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Creation of a PhenotypicGMM

Description

Creates an object of class PhenotypicGMM, a subclass of the class PhenotypicModel intended to represent the Generalist Matching Mutualism model of trait evolution on two specific trees.

Usage

createModelCoevolution(tree1, tree2, keyword)

Arguments

tree1	an object of class 'phylo' as defined in the R package 'ape'.
tree2	an object of class 'phylo' as defined in the R package 'ape'.
keyword	a string object. Defaut value "GMM" returns an object of class PhenotypicGMM, which takes advantage of faster distribution computation. Otherwise, a "PhenotypicModel" is returned, and the computation of the tip distribution will take much longer.

Value

an object of class "PhenotypicModel" or "PhenotypicGMM".

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 example trees
newick1 <- "(((A:1,B:1):3,(C:3,D:3):1):2,E:6);"
tree1 <- read.tree(text=newick1)
newick2 <- "((X:1.5,Y:1.5):3,Z:4.5);"
tree2 <- read.tree(text=newick2)

#Creating the model
modelGMM <- createModelCoevolution(tree1, tree2)

#Printing basic or full informations on the model definitions
show(modelGMM)
print(modelGMM)

#Simulates tip trait data
dataGMM <- simulateTipData(modelGMM, c(0,0,5,-5, 1, 1), method=2)

hmorlon/PANDA documentation built on April 24, 2024, 3:27 a.m.