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.
|Author||Daniel M. Griffith, Joseph A. Veech, and Charles J. Marsh|
|Date of publication||2016-02-09 20:53:56|
|Maintainer||Daniel M. Griffith <email@example.com>|
beetles: Beetle occurrence data from (Ulrich and Zalewski 2006).
cooccur: A function to calculate pairwise co-occurrence patterns from...
cooccur-package: cooccur: Probabilistic Species Co-occurrence Analysis in R
coprob: Internal function, not intended for use by the user.
coprobbase: Internal function, not intended for use by the user.
create.N.matrix: Function to create spp x spp matrix of potential co-occurring...
effect.sizes: Function to extract species pairwise effect sizes from an...
finches: Finch occurrence data from (Sanderson 2000).
obs.v.exp: Function to plot a visualization of the observed versus...
pair: Function to examine co-occurrence patterns for an individual...
pair.attributes: Function to create a species-wise summary of co-occurrence...
pair.profile: Function to produce a visualization of species contributions...
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...
rodents: Rodent occurrence data from (Brown and Kurzius 1987).
summary.cooccur: Method to summarize co-occurrence patterns.