R/betaLinker.R

In eliotmiller/metricTester: Test Metric and Null Model Statistical Performance

#' Run spatial simulations, null and beta metric calculations
#'
#' This function wraps a number of wrapper functions into one big metric + null 
#' tester function. Only a single test is performed, with results saved into memory.
#'
#' @param no.taxa The desired number of species in the input phylogeny
#' @param arena.length A numeric, specifying the length of a single side of the arena
#' @param mean.log.individuals Mean log of abundance vector from which species abundances
#' will be drawn
#' @param 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
#' @param sd.parameter Standard deviation of vector from which species' locations are 
#' drawn
#' @param max.distance The geographic distance within which neighboring
#' individuals should be considered to influence the individual in question
#' @param proportion.killed The percent of individuals in the total arena that should be
#' considered (as a proportion, e.g. 0.5 = half)
#' @param competition.iterations Number of generations over which to run competition 
#' simulations
#' @param no.plots Number of plots to place
#' @param plot.length Length of one side of desired plot
#' @param randomizations The number of randomized CDMs, per null, to generate. These are
#' used to compare the significance of the observed metric scores.
#' @param cores The number of cores to be used for parallel processing.
#' @param simulations 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).
#' @param nulls 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). 
#' @param metrics Optional. If not provided, defines the metrics as all of those in
#' defineBetaMetrics. If only a subset of those is desired, then metrics should take
#' the form of a character vector corresponding to named functions from defineBetaMetrics.
#' The available metrics can be determined by running names(defineBetaMetrics()).
#' 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).
#' 
#' @details This function wraps a number of other wrapper functions into
#' one big beta metric + null performance tester function. Only a single test is run, 
#' with results saved into memory. To perform multiple complete tests, use the
#' multiLinker function, which saves results to file.
#'
#' @return A list with two elements. The first is a list of data frames, with one for each
#' spatial simulation. These provide the observed beta metric scores for each spatial
#' simulation. The second level is a list of lists, one for each spatial simulation. Each
#' of these is a list of data frames. There is one data frame per null model, and it
#' summarizes the randomized metric scores for that null model for that spatial
#' simulation. Note that this is slightly different than the regular linker() function,
#' which does not output these raw metric scores (that function calculates SES and CI as
#' outputs).
#'
#' @export
#'
#' @importFrom geiger sim.bdtree
#'
#' @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
#' system.time(test <- betaLinker(no.taxa=50, arena.length=300, mean.log.individuals=2, 
#' 	length.parameter=5000, sd.parameter=50, max.distance=30, proportion.killed=0.2, 
#'	competition.iterations=3, no.plots=15, plot.length=30,
#'	randomizations=3, cores="seq", metrics=c("Pst", "Bst"),
#'	nulls=c("richness", "frequency")))

betaLinker <- function(no.taxa, arena.length, mean.log.individuals, length.parameter, 
	sd.parameter, max.distance, proportion.killed, competition.iterations, no.plots, 
	plot.length, randomizations, cores, simulations, nulls, metrics)
{
	#set these things to NULL if they are not passed in, meaning that all defined sims,
	#nulls and metrics will be calculated
	if(missing(simulations))
	{
		simulations <- NULL
	}
	if(missing(nulls))
	{
		nulls <- NULL
	}
	if(missing(metrics))
	{
		metrics <- NULL
	}

	#simulate tree with birth-death process
	tree <- sim.bdtree(b=0.1, d=0, stop="taxa", n=no.taxa)
	#prep the data for spatial simulations
	prepped <- prepSimulations(tree, arena.length, mean.log.individuals, length.parameter, 
		sd.parameter, max.distance, proportion.killed, competition.iterations)
	#run the spatial simulations
	arenas <- runSimulations(prepped, simulations)
	#derive CDMs. plots are placed in the same places across all spatial simulations
	cdms <- multiCDM(arenas, no.plots, plot.length)
	#calculate observed metrics for all three spatial simulations
	observed <- lapply(cdms, function(x) observedBetaMetrics(tree=tree, 
		picante.cdm=x$picante.cdm, metrics))
	#randomize all observed CDMs the desired number of times. this will generate a list of
	#lists of data frames. first level of list is for each spatial simulation (e.g. 3 if
	#there is random, habitat filtering and competitive exclusion). second level is for
	#randomizations, one for each. third level is data frames, one per null model
	allRandomizations <- lapply(1:length(cdms), function(x) betaMetricsNnulls(tree=tree, 
		picante.cdm=cdms[[x]]$picante.cdm,
		regional.abundance=cdms[[x]]$regional.abundance,
		distances.among=cdms[[x]]$dists, cores=cores, 
		randomizations=randomizations, metrics=metrics, nulls=nulls))
	#reduce the randomizations to a list of lists of (first order of lists is for each
	#spatial simulation) data frames
	reduced <- lapply(allRandomizations, reduceRandomizations)
	#give the names of the arenas (spatial sims) to the reduced results
	names(reduced) <- names(arenas)
	#unlike the regular linker function, do not run any of the error checking functions
	#on the results. return all results for now, will allow us to explore in more detail
	#later.
	results <- list("observed"=observed, "randomized"=reduced)
	results
}