Probabilistic Species Co-Occurrence Analysis in R

Documentation for package ‘cooccur’ version 1.3

cooccur-package	cooccur: Probabilistic Species Co-occurrence Analysis in R
beetles	Beetle occurrence data from (Ulrich and Zalewski 2006).
cooccur	A function to calculate pairwise co-occurrence patterns from a community dataset
create.N.matrix	Function to create spp x spp matrix of potential co-occurring sites (N) from a potential spp x site matrix.
effect.sizes	Function to extract species pairwise effect sizes from an object of class 'cooccur'.
finches	Finch occurrence data from (Sanderson 2000).
obs.v.exp	Function to plot a visualization of the observed versus expected oc-occurrences from an analysis stored in a 'coccurr' object.
pair	Function to examine co-occurrence patterns for an individual species.
pair.attributes	Function to create a species-wise summary of co-occurrence patterns.
pair.profile	Function to produce a visualization of species contributions to co-occurrence patterns.
plot.cooccur	Function for producing a heatmap co-occurrence visualization.
print.cooccur	Print significant pairwise species results.
prob.table	Function to extract the probability table from an analysis of species co-occurrence.
rodents	Rodent occurrence data from (Brown and Kurzius 1987).
summary.cooccur	Method to summarize co-occurrence patterns.