RPANDA (version 2.0)

PhenotypicModel-class: Class "PhenotypicModel"

Description

This class describes a model of phenotypic evolution running on a phylogenetic tree, with or without interactions between lineages.

Objects from the Class

Objects can be created by calls of the form new("PhenotypicModel", ...). Alternatively, you may just want to use the "createModel" function for predefined models.

Slots

name:

Object of class "character" ~~

period:

Object of class "numeric" ~~

aAGamma:

Object of class "function" ~~

numbersCopy:

Object of class "numeric" ~~

numbersPaste:

Object of class "numeric" ~~

initialCondition:

Object of class "function" ~~

paramsNames:

Object of class "character" ~~

constraints:

Object of class "function" ~~

params0:

Object of class "numeric" ~~

tipLabels:

Object of class "character" ~~

tipLabelsSimu:

Object of class "character" ~~

comment:

Object of class "character" ~~

Methods

[<-

signature(x = "PhenotypicModel", i = "ANY", j = "ANY", value = "ANY"): ...

[

signature(x = "PhenotypicModel", i = "ANY", j = "ANY", drop = "ANY"): ...

fitTipData

signature(object = "PhenotypicModel"): ...

getDataLikelihood

signature(object = "PhenotypicModel"): ...

getTipDistribution

signature(object = "PhenotypicModel"): ...

modelSelection

signature(object = "PhenotypicModel"): ...

print

signature(x = "PhenotypicModel"): ...

show

signature(object = "PhenotypicModel"): ...

simulateTipData

signature(object = "PhenotypicModel"): ...

References

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

Examples

# NOT RUN {
showClass("PhenotypicModel")
# }