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README.Rmd
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README.Rmd
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---
output: github_document
link-citations: yes
bibliography: vignettes/bib/biblio-jSDM.bib
biblio-style: vignettes/bib/jae.bst
csl: vignettes/bib/journal-of-applied-ecology.csl
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/"
)
```
# jSDM R Package <img src="man/figures/logo.png" align="right" alt="" width="120" />
[](https://github.com/ghislainv/jSDM/actions)
[](https://cran.r-project.org/package=jSDM)
[](https://doi.org/10.5281/zenodo.3253460)
[](https://cran.r-project.org/package=jSDM)
[](https://app.codecov.io/gh/ghislainv/jSDM?branch=master)
Package for fitting joint species distribution models (JSDM) in a hierarchical Bayesian framework [@Warton2015]. The Gibbs sampler is written in C++. It uses [Rcpp](https://cran.r-project.org/package=Rcpp), [Armadillo](https://arma.sourceforge.net/docs.html) and [GSL](https://www.gnu.org/software/gsl/) to maximize computation efficiency.
## System requirements
Make sure the GNU Scientific Library ([GSL](https://www.gnu.org/software/gsl/)) is installed on your system.
## Installation
### Stable version from CRAN
Install the latest stable version of **jSDM** from [CRAN](https://cran.r-project.org/) with:
```{r cran, eval=FALSE}
install.packages("jSDM")
```
### Development version
Or install the development version of **jSDM** from [GitHub](https://github.com/ghislainv/jSDM) with:
```{r github, eval=FALSE}
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 :
[jSDM_windows](https://nextcloud.fraisedesbois.net/index.php/s/bEQNBdwe2RCSK9F).
## 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](https://www.gnu.org/licenses/gpl-3.0.en.html) license. Anybody who is interested can contribute to the package development following our [Community guidelines](https://ecology.ghislainv.fr/jSDM/articles/Contributing.html). Every contributor must agree to follow the project’s [Code of Conduct](https://ecology.ghislainv.fr/jSDM/articles/Code_of_conduct.html).
## References