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ecoCopula

R package to find direct and indirect species associations from co-occurrence data

Installation

To install ecoCopula from CRAN:

install.packages("ecoCopula")

For the development version with the latest bells and whistles:

# install.packages("devtools")
devtools::install_github("eco-stats/ecoCopula")

For the development version with zero-inflated functionality:

# install.packages("devtools")
# devtools::install_github("r-forge/countreg/pkg")
devtools::install_github("eco-stats/ecoCopula", ref="e401671")

If you have trouble installing, please email me at g.popovic@unsw.edu.au.

Please note the original repository for this R package is found here

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Version

Install

install.packages('ecoCopula')

Monthly Downloads

345

Version

1.0.6

License

LGPL (>= 2.1)

Maintainer

David Warton

Last Published

December 4th, 2025

Functions in ecoCopula (1.0.6)

simulate.cord

Simulates new data from a given cord object
save_png

Function for saving png of biplot
summary.cord

Summary function for cgr object
residuals.stackedsdm

Calculate residuals from a stackedsdm object
predict.stackedsdm

Predictions from a stackedsdm object
print.cord

Print function for cord object
fitted.stackedsdm

Fitted values from a stackedsdm object
reexports

Objects exported from other packages
plot.cord

Plots an ordination of latent variables and their corresponding coefficients (biplot).
plot.cgr

Plot graph of direct species associations.
cgr

Fitting Gaussian copula graphical lasso to co-occurrence data
plot.stackedsdm

Plot residuals of stackedsdm.
print.cgr

Print function for cgr object
cord

Model based ordination with Gaussian copulas
summary.cgr

Summary function for cgr object
stackedsdm

Stacked species regression models, possibly fitted in parallel
spider

Spider data