This function runs multiple iterations of the linker function, saving results to file.
multiLinker(no.taxa, arena.length, mean.log.individuals, length.parameter,
sd.parameter, max.distance, proportion.killed, competition.iterations,
no.plots, plot.length, concat.by, randomizations, cores, iterations,
prefix, simulations, nulls, metrics)The desired number of species in the input phylogeny
A numeric, specifying the length of a single side of the arena
Mean log of abundance vector from which species abundances will be drawn
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
Standard deviation of vector from which species' locations are drawn
The geographic distance within which neighboring individuals should be considered to influence the individual in question
The percent of individuals in the total arena that should be considered (as a proportion, e.g. 0.5 = half)
Number of generations over which to run competition simulations
Number of plots to place
Length of one side of desired plot
Whether to concatenate the randomizations by richness, plot or both
The number of randomized CDMs, per null, to generate. These are used to compare the significance of the observed metric scores.
The number of cores to be used for parallel processing.
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.
Optional character vector to affix to the output RData file names, e.g. "test1".
Optional. If not provided, defines the simulations as all of those in defineSimulations. If only a subset of those simulations is desired, then simulations should take the form of a character vector corresponding to named functions from defineSimulations. The available simulations can be determined by running names(defineSimulations()). Otherwise, if the user would like to define a new simulation on the fly, the argument simulations can take the form of a named list of new functions (simulations).
Optional. If not provided, defines the nulls as all of those in defineNulls. If only a subset of those is desired, then nulls should take the form of a character vector corresponding to named functions from defineNulls. The available nulls can be determined by running names(defineNulls()). Otherwise, if the user would like to define a new null on the fly, the argument nulls can take the form of a named list of new functions (nulls).
Optional. If not provided, defines the metrics as all of those in defineMetrics. If only a subset of those is desired, then metrics should take the form of a character vector corresponding to named functions from defineMetrics. The available metrics can be determined by running names(defineMetrics()). Otherwise, if the user would like to define a new metric on the fly, the argument can take the form of a named list of new functions (metrics).
A list of lists of data frames. The first level of the output has one element for each simulation. The second level has one element for each null model. Each of these elements is a list of two data frames, one that summarizes the plot-level significance and another and arena-level significance.
This function wraps a number of other wrapper functions into one big metric + null performance tester function. Unlike the basic linker function, multiple tests can be run, with results saved as RDS files.
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
# NOT RUN {
#not run
#system.time(multiLinker(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, concat.by="richness",
#randomizations=3, cores="seq", iterations=2, prefix="test",
#nulls=c("richness", "frequency")))
# }
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