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 4.0.5 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 |

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.

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