glossa

1.2.4

User-Friendly 'shiny' App for Bayesian Species Distribution Models

0packages depend

3.1Kdownloads / year

84.1%test coverage

12/13checks pass

Overview

About

Maintained by Jorge Mestre-TomásFirst published 2024-10-157 releasesCRAN page ↗GitHub ↗

A user-friendly 'shiny' application for Bayesian machine learning analysis of marine species distributions. GLOSSA (Global Ocean Species Spatio-temporal Analysis) uses Bayesian Additive Regression Trees (BART; Chipman, George, and McCulloch (2010) doi:10.1214/09-AOAS285) to model species distributions with intuitive workflows for data upload, processing, model fitting, and result visualization. It supports presence-absence and presence-only data (with pseudo-absence generation), spatial thinning, cross-validation, and scenario-based projections. GLOSSA is designed to facilitate ecological research by providing easy-to-use tools for analyzing and visualizing marine species distributions across different spatial and temporal scales. Optionally, pseudo-absences can be generated within the environmental space using the external package 'flexsdm' (not on CRAN), which can be downloaded from https://github.com/sjevelazco/flexsdm; this functionality is used conditionally when available and all core features work without it.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("glossa", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("iMARES-group/glossa")

Development version from iMARES-group/glossa. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-glossa

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-glossa

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-glossa

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-release-macos-x86_64

Slowest check: 4.4 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.22

84.1%

Coverage · measured lines

Dependencies · direct

Check history

ERROR2026-05-02
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-13
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-30
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 2%

Downloads

3.1K

CRAN downloads in the past year

Rank #16,265 · ~8/day · ~255/mo

Releases R versions

Daily download trend is not available in this view yet.

21730 days

70390 days

3.1K1 year

Compare downloads with other packages →

Also on139 r2u17 autocran

Repository

GitHub ↗ imares-group/glossa

5Stars

1Forks

8Open issues

0Open PRs

7Releases

20Commits

1Contributors

License GPL-3.0 · 20 commits · Last activity 2026-04-17 · -16.7% stars, 30d

Stars over time

2025-06-25 · 22026-07-14 · 5

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/imares-group/glossa on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.1.0bs4Dash shiny

Imports (20)

automap blockCV dbarts dplyr DT GeoThinneR ggplot2 htmltools leaflet markdown mcp pROC sf shinyWidgets sparkline svglite terra tidyterra waiter zip

LinkingTo (0)

none

Suggests (8)

flexsdm jsonlite knitr matrixStats rmarkdown testthat tidyr tidyverse

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Jorge Mestre-Tomás

Author, Maintainer

Authors (2)

Jorge Mestre-Tomás

Author, Maintainer

Alba Fuster-Alonso

Author

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.2.4Latest
2025-09-19 · current release · diff ↗
1.2.3
2025-08-27 · diff ↗
unarchivedReturned to CRAN
2025-08-27
archivedRemoved from CRAN
2025-07-30
required archived package 'blockCV'
1.2.2
2025-07-15 · diff ↗
unarchivedReturned to CRAN
2025-07-15
archivedRemoved from CRAN
2025-06-30
requires archived package 'automap'
1.2.1
2025-06-20 · diff ↗
1.2.0
2025-06-17 · diff ↗
1.1.0
2025-05-28 · diff ↗
unarchivedReturned to CRAN
2025-05-28
archivedRemoved from CRAN
2025-05-08
issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
1.0.0
2024-10-15
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-10-15
Total releases: 7 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 1.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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