CreateClassObject function

Create class object

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

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)

Returns

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)

Details

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

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

Author(s)

Jonathan Drury jonathan.p.drury@gmail.com

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)