Package for fitting joint species distribution models (JSDM) in ahierarchical Bayesian framework (Wartonetal. 2015). The Gibbs sampler is written in C++. It usesRcpp,Armadillo andGSL to maximize computationefficiency.
Make sure the GNU Scientific Library (GSL) is installed on yoursystem.
Install the latest stable version ofjSDM fromCRAN with:
install.packages("jSDM")Or install the development version ofjSDM fromGitHub with:
devtools::install_github("ghislainv/jSDM")The package includes the following functions to fit various speciesdistribution models :
| function | data type | data format |
|---|---|---|
jSDM_binomial_logit() | presence-absence | wide |
jSDM_binomial_probit() | presence-absence | wide |
| presence-absence | wide | |
| presence-absence | long | |
jSDM_poisson_log() | abundance | wide |
jSDM_gaussian() | continuous | wide |
ThejSDM R package is Open Source and released under theGNU GPL version3 license. Anybody who is interested can contribute to the packagedevelopment following ourCommunityguidelines. Every contributor must agree to follow the project’sCodeof Conduct.