RPANDA (version 1.9)

sim.divergence.geo: Simulation of trait data under the model of divergent character displacement described in Drury et al. 2017

Description

Simulates the evolution of a continuous character under a model of evolution where trait values are repelled according to between-species similarity in trait values, taking into account biogeography using a biogeo.object formatted from RPANDA (see CreateGeoObject function in RPANDA package)

Usage

sim.divergence.geo(phylo,pars, Nsegments=2500, plot=FALSE, geo.object)

Arguments

phylo

a phylogenetic tree

pars

A matrix with a number of rows corresponding to the desired number of simulations, columns containing values for \(sig2\) in [,1], \(m\) in [,2], \(alpha\) in [,3], root.value in [,4], \(psi\) of the OU model in [,5], and \(theta\) in the OU model in [,6]

Nsegments

the minimum number of time steps to simulate

plot

logical indicating whether to plot the simulated trait values at each time step

geo.object

geography object created using CreateGeoObject

Value

A matrix with the simulated values for each lineage (one simulation per row; columns correspond to species)

Details

Adjusting Nsegments will impact the length of time the simulations take. The length of each segment (max(nodeHeights(phylo))/Nsegments) should be much smaller than the smallest branch (min(phylo$edge.length)).

References

Drury, J., Grether, G., Garland Jr., T., and Morlon, H. 2017. A review of phylogenetic methods for assessing the influence of interspecific interactions on phenotypic evolution. Systematic Biology

See Also

CreateGeoObject

Examples

# NOT RUN {
data(Anolis.data)
phylo<-Anolis.data$phylo
geo.object<-Anolis.data$geography.object

#simulate with the OU process present and absent
pars<-expand.grid(0.05,2,1,0,c(2,0),0)
sim.divergence.geo(phylo,pars,Nsegments=2500, plot=FALSE, geo.object)
# }
# NOT RUN {
# }