Usage
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)
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
concat.by
Whether to concatenate the randomizations by richness, plot or both
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. 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).
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).
metrics
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).