jSDM R Package
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 4.3.0 can be found here :
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 |
jSDM_gaussian() | continuous | 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.