metricTester (version 1.3.6)

prepSimulations: Prep data for spatial simulations

Description

Given the required parameters for defined spatial simulations, will prepare an object of class simulations.input for actual simulation.

Usage

prepSimulations(tree, arena.length, mean.log.individuals, length.parameter,
  sd.parameter, max.distance, proportion.killed, competition.iterations)

Arguments

tree

Phylo object

arena.length

A numeric, specifying the length of a single side of the arena

mean.log.individuals

Mean log of abundance vector from which species abundances will be drawn

length.parameter

Length of vector from which species' locations are drawn. Large values of this parameter dramatically decrease the speed of the function but result in nicer looking communities

sd.parameter

Standard deviation of vector from which species' locations are drawn

max.distance

The geographic distance within which neighboring individuals should be considered to influence the individual in question

proportion.killed

The percent of individuals in the total arena that should be considered (as a proportion, e.g. 0.5 = half)

competition.iterations

Number of generations over which to run competition simulations

Value

A prepared simulations.input object

Details

This function preps the input for any of the spatial simulations as defined in defineSimulations. If additional parameters are ever required for those simulations, they would have to be added as additional arguments here.

References

Miller, E. T., D. R. Farine, and C. H. Trisos. 2016. Phylogenetic community structure metrics and null models: a review with new methods and software. Ecography DOI: 10.1111/ecog.02070

Examples

# NOT RUN {
tree <- geiger::sim.bdtree(b=0.1, d=0, stop="taxa", n=50)

prepped <- prepSimulations(tree, arena.length=300, mean.log.individuals=2, 
	length.parameter=5000, sd.parameter=50, max.distance=20, proportion.killed=0.2,
competition.iterations=3)
# }