CreateClassObject: Create class object

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

Create class object

Description

This function returns names of internode intervals, named descendants of each node, and a class object formatted in a way that can be passed to CreateGeobyClassObject

Usage

CreateClassObject(map,rnd=5,return.mat=FALSE)

Arguments

map	stochastic map from make.simmap in phytools
rnd	integer indicating the number of decimal places to which times should be rounded (default value is 5) (see round)
return.mat	logical indicating whether to return simmap in a format to be passed to other internal functions (usually FALSE)

Details

This function formats the class object so that it can be correctly passed to the numerical integration performed in fit_t_comp_subgroup.

Value

a list with the following components:

class.object	a list of matrices specifying the state of each branch during each internode interval (see Details)
times	a vector containing the time since the root of the tree at which nodes or changes in biogeography occur (used internally in other functions)
spans	a vector specifying the distances between times (used internally in other functions)

Author(s)

Jonathan Drury [e-mail]

References

Drury, J., Tobias, J., Burns, K., Mason, N., Shultz, A., and Morlon, H. in review. Contrasting impacts of competition on ecological and social trait evolution in songbirds. PLOS Biology.

Drury, J., Clavel, J., Manceau, M., and Morlon, H. 2016. Estimating the effect of competition on trait evolution using maximum likelihood inference. Systematic Biology doi 10.1093/sysbio/syw020

See Also

fit_t_comp_subgroup,CreateGeobyClassObject

Examples

data(Anolis.data)

#Create a make.simmap object
require(phytools)
geo<-c(rep("cuba",7),rep("hispaniola",9),"puerto_rico")
names(geo)<-Anolis.data$phylo$tip.label
stochastic.map<-phytools::make.simmap(Anolis.data$phylo, 
									geo, model="ER", nsim=1)
CreateClassObject(stochastic.map)

hmorlon/PANDA documentation built on March 8, 2024, 8:36 p.m.