Probabilistic Species Co-Occurrence Analysis in R
cooccur: Probabilistic Species Co-occurrence Analysis in R
A function to calculate pairwise co-occurrence patterns from a communi...
Internal function, not intended for use by the user.
Internal function, not intended for use by the user.
Function to create spp x spp matrix of potential co-occurring sites (N...
Function to extract species pairwise effect sizes from an object of cl...
Function to plot a visualization of the observed versus expected oc-oc...
Function to create a species-wise summary of co-occurrence patterns.
Function to produce a visualization of species contributions to co-occ...
Function to examine co-occurrence patterns for an individual species.
Function for producing a heatmap co-occurrence visualization.
Print significant pairwise species results.
Function to extract the probability table from an analysis of species ...
Method to summarize co-occurrence patterns.
This R package applies the probabilistic model of species co-occurrence (Veech 2013) to a set of species distributed among a set of survey or sampling sites. The algorithm calculates the observed and expected frequencies of co-occurrence between each pair of species. The expected frequency is based on the distribution of each species being random and independent of the other species. The analysis returns the probabilities that a more extreme (either low or high) value of co-occurrence could have been obtained by chance. The package also includes functions for visualizing species co-occurrence results and preparing data for downstream analyses.