sim.divergence.geo: Simulation of trait data under the model of divergent...

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

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

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)).

Value

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

Author(s)

J.P. Drury [e-mail] F. Hartig

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

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)

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