createModel: Creation of a PhenotypicModel

In RPANDA: Phylogenetic ANalyses of DiversificAtion

Creation of a PhenotypicModel

Description

Creates an object of class PhenotypicModel, intended to represent a model of trait evolution on a specific tree. DIstinct keywords correspond to different models, using one phylogenetic tree.

Usage

createModel(tree, keyword)

Arguments

tree	an object of class 'phylo' as defined in the R package 'ape'.
keyword	a string specifying the model. Available models include "BM", "BM_from0", "BM_from0_driftless", "OU", "OU_from0", "ACDC", "DD", "PM", "PM_OUless".

Value

the object of class "PhenotypicModel".

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')

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

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