cooccur: Probabilistic Species Co-Occurrence Analysis in R

Share:

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 <griffith.dan@gmail.com>
License
GPL-2
Version
1.3

View on CRAN

Man pages

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.

Files in this package

cooccur
cooccur/inst
cooccur/inst/CITATION
cooccur/NAMESPACE
cooccur/data
cooccur/data/rodents.rda
cooccur/data/finches.rda
cooccur/data/beetles.rda
cooccur/R
cooccur/R/plot.cooccur.R
cooccur/R/prob.table.R
cooccur/R/effect.sizes.R
cooccur/R/pair.profile.R
cooccur/R/obs.v.exp.R
cooccur/R/cooccur-internal.R
cooccur/R/cooccur.R
cooccur/R/summary.cooccur.R
cooccur/R/print.cooccur.R
cooccur/R/pair.R
cooccur/R/coprob.R
cooccur/R/pair.attributes.R
cooccur/R/coprobbase.R
cooccur/R/create.N.matrix.R
cooccur/MD5
cooccur/DESCRIPTION
cooccur/man
cooccur/man/coprobbase.Rd
cooccur/man/obs.v.exp.Rd
cooccur/man/summary.cooccur.Rd
cooccur/man/pair.Rd
cooccur/man/cooccur.Rd
cooccur/man/plot.cooccur.Rd
cooccur/man/finches.Rd
cooccur/man/effect.sizes.Rd
cooccur/man/rodents.Rd
cooccur/man/pair.profile.Rd
cooccur/man/create.N.matrix.Rd
cooccur/man/print.cooccur.Rd
cooccur/man/pair.attributes.Rd
cooccur/man/beetles.Rd
cooccur/man/cooccur-package.Rd
cooccur/man/prob.table.Rd
cooccur/man/coprob.Rd