Package: ecoCopula 1.0.6

David Warton

ecoCopula: Graphical Modelling and Ordination using Copulas

Creates 'graphs' of species associations (interactions) and ordination biplots from co-occurrence data by fitting discrete gaussian copula graphical models. Methods described in Popovic, GC., Hui, FKC., Warton, DI., (2018) <doi:10.1016/j.jmva.2017.12.002>.

Authors:Gordana Popovic [aut], David Warton [ctb, cre], Francis K.C. Hui [ctb], Michelle Lim [ctb]

ecoCopula_1.0.6.tar.gz
ecoCopula_1.0.6.zip(r-4.7)ecoCopula_1.0.6.zip(r-4.6)ecoCopula_1.0.6.zip(r-4.5)
ecoCopula_1.0.6.tgz(r-4.6-any)ecoCopula_1.0.6.tgz(r-4.5-any)
ecoCopula_1.0.6.tar.gz(r-4.7-any)ecoCopula_1.0.6.tar.gz(r-4.6-any)
ecoCopula_1.0.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ecoCopula/json (API)

# Install 'ecoCopula' in R:

install.packages('ecoCopula', repos = c('https://eco-stats.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/eco-stats/ecocopula/issues

Pkgdown/docs site:https://eco-stats.github.io

Datasets:

spider - Spider data

On CRAN:

6.30 score 2 packages 55 scripts 505 downloads 1 mentions 15 exports 44 dependencies

Last updated from:f59fc2595c. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	174
source / vignettes	OK	207
linux-release-x86_64	OK	197
macos-release-arm64	OK	196
macos-oldrel-arm64	OK	220
windows-devel	OK	119
windows-release	OK	114
windows-oldrel	OK	109
wasm-release	OK	158

Exports:cgr cord fitted.stackedsdm ldTweedie plot.cgr plot.cord plot.stackedsdm predict.stackedsdm print.cgr print.cord residuals.stackedsdm simulate.cord stackedsdm summary.cgr summary.cord

Dependencies:betareg cli coda codetools cpp11 doParallel flexmix foreach Formula glasso glm2 glue igraph iterators lattice lifecycle lmtest magrittr MASS Matrix mgcv modeltools mvabund network nlme nnet numDeriv ordinal pillar pkgconfig plyr Rcpp RcppGSL rlang sandwich sna statmod statnet.common tibble tweedie ucminf utf8 vctrs zoo

ecoCopula package for model based ordination and graphical modelling in ecology

Rendered fromecoCopula.Rmdusingknitr::rmarkdown

Last update: 2025-12-03
Started: 2024-02-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Fitting Gaussian copula graphical lasso to co-occurrence data	cgr
Model based ordination with Gaussian copulas	cord
Fitted values from a stackedsdm object	fitted.stackedsdm
Plot graph of direct species associations.	plot.cgr
Plots an ordination of latent variables and their corresponding coefficients (biplot).	plot.cord
Plot residuals of stackedsdm.	plot.stackedsdm
Predictions from a stackedsdm object	predict.stackedsdm
Print function for cgr object	print.cgr
Print function for cord object	print.cord
Calculate residuals from a stackedsdm object	residuals.stackedsdm
Simulates new data from a given cord object	simulate.cord
Spider data	spider
Stacked species regression models, possibly fitted in parallel	stackedsdm
Summary function for cgr object	summary.cgr
Summary function for cgr object	summary.cord