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Last data update: 2014.03.03

R: Run multiple simulations and calculations to test beta metric...

betaMultiLinker

R Documentation

Run multiple simulations and calculations to test beta metric + null performance

Description

This function runs multiple iterations of the linker function, saving results to file.

Usage

betaMultiLinker(no.taxa, arena.length, mean.log.individuals, length.parameter,
  sd.parameter, max.distance, proportion.killed, competition.iterations,
  no.plots, plot.length, randomizations, cores, iterations, prefix, simulations,
  nulls, metrics)

Arguments

`no.taxa`	The desired number of species in the input phylogeny
`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 indivduals 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
`no.plots`	Number of plots to place
`plot.length`	Length of one side of desired plot
`randomizations`	The number of randomized CDMs, per null, to generate. These are used to compare the significance of the observed metric scores.
`cores`	The number of cores to be used for parallel processing.
`iterations`	The number of complete tests to be run. For instance, 1 iteration would be considered a complete cycle of running all spatial simulations, randomly placing plots in the arenas, sampling the contents, creating a community data matrix, calculating observed metric scores, then comparing these to the specified number of randomizations of the original CDMs.
`prefix`	Optional character vector to affix to the output RData file names, e.g. "test1".
`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.
`nulls`	Optional list of named null model functions to use. If invoked, this option will likely be used to run a subset of the defined null models.
`metrics`	Optional list of named metric functions to use. If invoked, this option will likely be used to run a subset of the defined metrics.

Details

This function wraps a number of other wrapper functions into one big beta metric + null performance tester function. Unlike the basic betaLinker function, multiple tests can be run, with results saved as RDS files.

Value

Multiple iterations of the the betaLinker function.

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

#not run
#system.time(betaMultiLinker(no.taxa=50, arena.length=300, mean.log.individuals=3.2, 
	#length.parameter=5000, sd.parameter=50, max.distance=20, proportion.killed=0.3, 
#competition.iterations=2, no.plots=20, plot.length=30,
#randomizations=3, cores="seq", iterations=2, prefix="test",
#nulls=list("richness"=metricTester:::my_richnessNull,
#"frequency"=metricTester:::my_frequency)))