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:

install.packages("jSDM")

### 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 4.0.3 can be found here :

## Available functions

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

function data type
jSDM_binomial_logit presence-absence
jSDM_binomial_probit_block presence-absence
jSDM_binomial_probit_block_long_format presence-absence
jSDM_poisson_log abundance

## 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. (2015) So many variables: Joint modeling in community ecology. Trends in Ecology & Evolution, 30, 766–779.