RPANDA (version 1.9)

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

Description

Simulates the evolution of a continuous character that evolves depending on pairwise similarity in another, OU-evolving trait (e.g., a trait that covaries with resource use). sig2 and z0 are shared between two traits, max and alpha are for focal trait, OU parameters for non-focal trait

Usage

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

Arguments

phylo

an object of type 'phylo' (see ape documentation)

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 for the non-focal, resource use trait in [,5], and \(theta\) in the OU model for the non-focal resource use trait in [,6]

Nsegments

the minimum number of time steps to simulate

plot

if TRUE, returns two plots: the top plot is focal trait undergoing convergence, the bottom plot is non-focal trait evolving under BM or OU

geo.object

geography object created using CreateGeoObject

Value

A list of two matrices with the simulated values for each lineage (one simulation per row; columns correspond to species) for trait1 (focul trait undergoing convergence) and non.focal (resource-use trait that determines strength of convergence in trait1)

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,-0.1,1,0,c(2,0),0)
sim.convergence.geo(phylo,pars,Nsegments=2500, plot=FALSE, geo.object)
# }
# NOT RUN {
# }