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cooccur  

Probabilistic Species Co-Occurrence Analysis in R
View on CRAN: Click here


Download and install cooccur package within the R console
Install from CRAN:
install.packages("cooccur")

Install from Github:
library("remotes")
install_github("cran/cooccur")

Install by package version:
library("remotes")
install_version("cooccur", "1.3")



Attach the package and use:
library("cooccur")
Maintained by
Daniel M. Griffith
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-03-09
Latest Update:
Description:
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.
How to cite:
Daniel M. Griffith (2014). cooccur: Probabilistic Species Co-Occurrence Analysis in R. R package version 1.3, https://cran.r-project.org/web/packages/cooccur. Accessed 26 Aug. 2026.
Previous versions and publish date:
(2026-07-09 07:28), 1.0 (2014-03-09 16:43), 1.1 (2014-05-06 15:10), 1.2 (2014-11-18 11:28), 1.3 (2016-02-09 20:53)
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Complete documentation for cooccur
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