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.
Make sure the GNU Scientific Library (GSL) is installed on your system.
Install the latest stable version of jSDM from CRAN with:
install.packages("jSDM")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 :
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 |
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.
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.