EcoSimR (version 0.1.0)

niche_null_model: Niche overlap null models

Description

Create a null model for niche overlap; choices of algorithm and metric are constrained to be valid for niche null models.

Usage

niche_null_model(speciesData, algo = "ra3", metric = "pianka", nReps = 1000, saveSeed = FALSE, algoOpts = list(), metricOpts = list(), suppressProg = FALSE)

Arguments

speciesData

a data frame in which each row is a species, each column is a resource utilization category, and the entries represent the quantity of the resource used by each species. Examples might be the amount of time a species spends foraging in different microhabitats, the biomass of different prey types, or counts of the number of times an adult female oviposits eggs on different species of a host plant.

algo

the algorithm to use, must be "ra1", "ra2", "ra3", "ra4"; default is "ra3".

metric

the metric used to calculate the null model: choices are "pianka", "czekanowski", "pianka_var", "czekanowski_var", "pianka_skew", "czekanowski_skew"; default is "pianka".

nReps

the number of replicate null assemblages to create; default is 1000 replicates.

saveSeed

TRUE or FALSE. If TRUE the current seed is saved so the simulation can be repeated; default is FALSE.

algoOpts

a list containing all the options for the specific algorithm you want to use. Must match the algorithm given in the `algo` argument.

metricOpts

a list containing all the options for the specific metric you want to use. Must match the metric given in the `metric` argument.

suppressProg

TRUE or FALSE. If true, display of the progress bar in the console is suppressed; default is FALSE. This setting is useful for creating markdown documents with `knitr`.

Examples

## Not run: 
# ## Load MacAruthur warbler data
# data(dataMacWarb)
# 
# ## Run the null model
# warbMod <- niche_null_model(dataMacWarb,nReps=1000)
# ## Summary and plot info
# summary(warbMod)
# plot(warbMod)
# plot(warbMod,type="niche")
# ## End(Not run)