Probabilistic Species Co-Occurrence Analysis in R

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Documentation for package ‘cooccur’ version 1.3

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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.