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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("gordy2x/ecoCopula")

For the development version with zero-inflated functionality:

# install.packages("devtools")
# devtools::install_github("r-forge/countreg/pkg")
devtools::install_github("gordy2x/ecoCopula", ref="e401671")

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

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Version

Install

install.packages('ecoCopula')

Monthly Downloads

379

Version

1.0.2

License

LGPL (>= 2.1)

Maintainer

Gordana Popovic

Last Published

March 2nd, 2022

Functions in ecoCopula (1.0.2)

cgr

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

Predictions from a stackedsdm object
cord

Model based ordination with Gaussian copulas
spider

Spider data
print.cgr

Print function for cgr object
plot.cgr

Plot graph of direct species associations.
fitted.stackedsdm

Fitted values from a stackedsdm object
stackedsdm

Stacked species regression models, possibly fitted in parallel
summary.cgr

Summary function for cgr object
summary.cord

Summary function for cgr object
print.cord

Print function for cord object
reexports

Objects exported from other packages
simulate.cord

Simulates new data from a given cord object
residuals.stackedsdm

Calculate residuals from a stackedsdm object
plot.cord

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

Plot residuals of stackedsdm.