Package for fitting joint species distribution models (JSDM) in a hierarchical Bayesian framework (Warton et al. 2015). The Gibbs sampler is written in C++. It uses Rcpp, Armadillo and GSL to maximize computation efficiency.

System requirements

Make sure the GNU Scientific Library (GSL) is installed on your system.

Installation

Stable version from CRAN

Install the latest stable version of jSDM from CRAN with:

Development version

Or install the development version of jSDM from GitHub with:

devtools::install_github("ghislainv/jSDM")

Or the binary release of jSDM’s development version compiled with R version 4.0.5 can be found here :

jSDM_windows.

Available functions

The package includes the following functions to fit various species distribution models :

function data type data format
jSDM_binomial_logit() presence-absence wide
jSDM_binomial_probit() presence-absence wide
jSDM_binomial_probit_sp_constrained() presence-absence wide
jSDM_binomial_probit_long_format() presence-absence long
jSDM_poisson_log() abundance wide

Contributing

The jSDM R package is Open Source and released under the GNU GPL version 3 license. Anybody who is interested can contribute to the package development following our Community guidelines. Every contributor must agree to follow the project’s Code of Conduct.

References

Warton, D.I., Blanchet, F.G., O’Hara, R.B., Ovaskainen, O., Taskinen, S., Walker, S.C. & Hui, F.K.C. (2015) So many variables: Joint modeling in community ecology. Trends in Ecology & Evolution, 30, 766–779.