cooccur: Probabilistic Species Co-Occurrence Analysis in R
Version 1.3

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("cooccur")

Getting started

Package overview

Popular man pages

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.
effect.sizes: Function to extract species pairwise effect sizes from an...
plot.cooccur: Function for producing a heatmap co-occurrence visualization.
prob.table: Function to extract the probability table from an analysis of...
summary.cooccur: Method to summarize co-occurrence patterns.
See all...

All man pages Function index File listing

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.

Functions

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

Files

inst
inst/CITATION
NAMESPACE
data
data/rodents.rda
data/finches.rda
data/beetles.rda
R
R/plot.cooccur.R
R/prob.table.R
R/effect.sizes.R
R/pair.profile.R
R/obs.v.exp.R
R/cooccur-internal.R
R/cooccur.R
R/summary.cooccur.R
R/print.cooccur.R
R/pair.R
R/coprob.R
R/pair.attributes.R
R/coprobbase.R
R/create.N.matrix.R
MD5
DESCRIPTION
man
man/coprobbase.Rd
man/obs.v.exp.Rd
man/summary.cooccur.Rd
man/pair.Rd
man/cooccur.Rd
man/plot.cooccur.Rd
man/finches.Rd
man/effect.sizes.Rd
man/rodents.Rd
man/pair.profile.Rd
man/create.N.matrix.Rd
man/print.cooccur.Rd
man/pair.attributes.Rd
man/beetles.Rd
man/cooccur-package.Rd
man/prob.table.Rd
man/coprob.Rd
cooccur documentation built on May 19, 2017, 6:36 p.m.

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