metricTester (version 1.2.2)

runSimulations: Run defined spatial simulations

Description

Given a prepared simulations.input object, will run all simulations defined in defineSimulations, and return a list of randomized CDMs.

Usage

runSimulations(simulations.input, simulations)

Arguments

simulations.input

A prepared simulations.input object, as generated by prepSimulations.

simulations

Optional list of named spatial simulation functions to use. These must be defined in the defineSimulations function. If invoked, this option will likely be used to run a subset of the defined spatial simulations.

Value

A list of lists of simulation results, where each of the first-order elements in the list relates to a unique simulation as defined in defineSimulations.

Details

Currently we are running 3 spatial simulations. This function first confirms that the input is of class simulations.input and, if so, then confirms that the simulations are in a named list (via checkSimulations), then lapplies all spatial simulation functions to the input object.

References

Miller, E. T., D. R. Farine, and C. H. Trisos. 2015. Phylogenetic community structure metrics and null models: a review with new methods and software. bioRxiv 025726.

Examples

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)

#not run
results <- runSimulations(prepped)