glossa

GLOSSA: a user-friendly R Shiny application for Bayesian machine learning analysis of marine species distribution

https://github.com/imares-group/glossa

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GLOSSA: a user-friendly R Shiny application for Bayesian machine learning analysis of marine species distribution

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# GLOSSA - Global Ocean Species Spatio-temporal Analysis 


[![CRAN status](https://www.r-pkg.org/badges/version/glossa)](https://CRAN.R-project.org/package=glossa)
[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
[![R-CMD-check](https://github.com/iMARES-group/glossa/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/iMARES-group/glossa/actions/workflows/R-CMD-check.yaml)


***

**GLOSSA** (Global Ocean Species Spatio-temporal Analysis) is an open-source, user-friendly R Shiny application designed for modeling marine species distribution. Written in R, GLOSSA uses the Shiny and bs4Dash libraries to provide an intuitive interface for fitting species distribution models using presence/absence or presence-only (pseudo-absences will be generated) data. The app uses flexible machine learning techniques like Bayesian Additive Regression Trees (BART), enabling users to model species distributions across different temporal and spatial scales and forecast future scenarios based on environmental data. With GLOSSA, users can explore current and future suitable habitats and visualize results with minimal coding expertise.

![](https://github.com/iMARES-group/glossa/blob/main/inst/app/www/img/glossa_short_flowchart.png)

## Getting started

You can install and run GLOSSA using the following R code:

```r
install.packages("glossa")

library(glossa)
run_glossa()
```

To install the development version of GLOSSA from GitHub, use:

```r
if (!require("devtools")) 
  install.packages("devtools")

devtools::install_github("iMARES-group/glossa")
```

## Documentation and resources

For detailed documentation, tutorials, and examples on how to use **GLOSSA**, visit the [official website](https://iMARES-group.github.io/glossa/):

* [Overview](https://iMARES-group.github.io/glossa/)
* [Installation and getting started guide](https://iMARES-group.github.io/glossa/get_started.html)
- [Full documentation](https://iMARES-group.github.io/pages/documentation/)
- [Tutorials and examples](https://iMARES-group.github.io/glossa/pages/tutorials_examples/)

### Current version

* **Development version** in progress (27/08/2025)
* CRAN release: **v1.2.3** (27/08/2024)

See the full [changelog](https://github.com/iMARES-group/glossa/blob/main/NEWS.md)

## How to cite GLOSSA

The GLOSSA manuscript is currently in progress. In the meantime, you can cite the [preprint](https://doi.org/10.48550/arXiv.2505.05862) as follows:

> Mestre-Tomás, J., Fuster-Alonso, A., Bellido, J. M., and Coll, M. (2025). GLOSSA: a user-friendly R Shiny application for Bayesian machine learning analysis of marine species distribution. arXiv preprint arXiv:2505.05862. DOI: https://doi.org/10.48550/arXiv.2505.05862

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