create.pool: Simulates a species pool
In VirtualCom: Assembling virtual plant communities

Description Usage Arguments Details Value See Also Examples

Simulates a species pool containing a phylogeny, species trait values and information on invasion status.

1 2	create.pool(n.species.pool, n.invader.pool, evol.model, min.phyl.signal, evol.model.param, nrep = 499)

`n.species.pool`	number of species (natives and invaders)
`n.invader.pool`	number of invaders
`evol.model`	choice of evolutionary model which determines phylogenetic signal, see details
`min.phyl.signal`	minimum level of phylogenetic signal accepetd, if min.phyl.signal=NA no minimum limit
`evol.model.param`	applies only if evol.model is different from Brownian motion, see details
`nrep`	number of repetition for phylogenetic signal and tree imbalance tests

The different evolutionary models (argument: evol.mod) are based on tree transformations. These are done using the function rescale in the geiger package and are coded as follows: "1" = BM (Brownian motion), "2" = deltaTree, "3" = kappaTree, "4" = ouTree, 5 = "lambdaTree". The tree transformations can be parameterized using the argument evol.model.param.

List of objects:

func: evolved functional traits for each species of the pool
phylo: phylogenetic tree of the species pool
indices: results of phylogenetic signal and colless test for phylogenetic tree shape
invader: list of the invader's identities and trait values
parameters: the parameters used for creating the species pool

simulation.experiment for running simulation experiments with an integrated simulation of species pools and diversity analyses of final community structures.

pool <- create.pool(n.species.pool=500, n.invader.pool=1, evol.model="deltaTree", min.phyl.signal=NA, evol.model.param=0.1, nrep=1)
# plot tree
plot(pool$phy)
# calculate phylogenetic signal
phylosignal(pool$func$niche_evol, pool$phy, checkdata=FALSE)