niche_null_model: Niche overlap null models

Description Usage Arguments Examples

View source: R/niche_overlap_null.R

Description

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

Usage

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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

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## 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)

Example output

Loading required package: MASS
Warning message:
In data(dataMacWarb) : data set 'dataMacWarb' not found

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Time Stamp:  Tue Oct 10 02:24:52 2017 
Reproducible:  FALSE 
Number of Replications:  1000 
Elapsed Time:  0.3 secs 
Metric:  pianka 
Algorithm:  ra3 
Observed Index:  0.55514 
Mean Of Simulated Index:  0.38674 
Variance Of Simulated Index:  0.002383 
Lower 95% (1-tail):  0.31868 
Upper 95% (1-tail):  0.46973 
Lower 95% (2-tail):  0.30973 
Upper 95% (2-tail):  0.50096 
Lower-tail P =  0.994 
Upper-tail P =  0.006 
Observed metric > 994 simulated metrics 
Observed metric < 6 simulated metrics 
Observed metric = 0 simulated metrics 
Standardized Effect Size (SES):  3.4495 

EcoSimR documentation built on May 29, 2017, 9:11 p.m.