Package: ecoCopula 1.0.2

Gordana Popovic

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, cre], David Warton [ctb], Francis K.C. Hui [ctb], Michelle Lim [ctb]

ecoCopula_1.0.2.tar.gz
ecoCopula_1.0.2.tar.gz(r-4.5-noble)ecoCopula_1.0.2.tar.gz(r-4.4-noble)
ecoCopula_1.0.2.tgz(r-4.4-emscripten)ecoCopula_1.0.2.tgz(r-4.3-emscripten)
ecoCopula.pdf |ecoCopula.html✨
ecoCopula/json (API)
NEWS

# Install 'ecoCopula' in R:

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

Datasets:

spider - Spider data

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.48 score 2 packages 304 downloads 1 mentions 15 exports 45 dependencies

Last updated 3 years agofrom:9e4fd18a2b. Checks:2 OK, 1 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 27 2025
R-4.5-linux	NOTE	Mar 27 2025
R-4.4-linux	OK	Mar 27 2025

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 fansi 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 fromthe_basics.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2022-03-01
Started: 2020-11-10

Citation

To cite ecoCopula in publications use:

Popovic, GC, Warton, DI, Thomson, FJ, Hui, FKC, Moles, AT. Untangling direct species associations from indirect mediator species effects with graphical models. Methods Ecol Evol. 2019; 10: 1571– 1583.

Corresponding BibTeX entry:

  @Article{,
    title = {Untangling direct species associations from indirect
      mediator species effects with graphical models},
    author = {Gordana C. Popovic and David I. Warton and Fiona J.
      Thomson and Angela T. Moles},
    journal = {Methods in Ecology and Evolution},
    year = {2019},
    volume = {10},
    number = {9},
    pages = {1571 -- 1583},
    doi = {10.1111/2041-210X.13247},
  }

Readme and manuals

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

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