Probabilistic Species Co-occurrence Analysis in R

Documentation for package ‘cooccur’ version 1.0

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
coprob	Internal function, not intended for use by the user.
coprobbase	Internal function, not intended for use by the user.
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.