cooccur: Probabilistic Species Co-Occurrence Analysis in R

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.

AuthorDaniel M. Griffith, Joseph A. Veech, and Charles J. Marsh
Date of publication2016-02-09 20:53:56
MaintainerDaniel M. Griffith <griffith.dan@gmail.com>
LicenseGPL-2
Version1.3

View on CRAN

Functions

beetles Man page
cooccur Man page
cooccur Man page
cooccur-package Man page
coprob Man page
coprobbase Man page
create.N.matrix Man page
effect.sizes Man page
finches Man page
obs.v.exp Man page
pair Man page
pair.attributes Man page
pair.profile Man page
plot.cooccur Man page
print.cooccur Man page
prob.table Man page
rodents Man page
summary.cooccur Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.