Learn R Programming

glossa (version 1.2.4)

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

Description

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) ) 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 ; this functionality is used conditionally when available and all core features work without it.

Copy Link

Version

Install

install.packages('glossa')

Monthly Downloads

108

Version

1.2.4

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Jorge Mestre-Tomás

Last Published

September 19th, 2025

Functions in glossa (1.2.4)

generate_pa_env_space_flexsdm

Generate Environmental-space Pseudo-Absences via flexsdm (per temporal stratum)
generate_pa_target_group

Generate Pseudo-Absences Using Target-Group Background
generate_pa_random

Generate Random Pseudo-Absences
file_input_area_server

Server-side Logic for Custom File Input
invert_polygon

Invert a Polygon
file_input_area_ui

Custom File Input UI
generate_prediction_plot

Generate Prediction Plot
getFprTpr

Compute specificity and sensitivity
glossa_analysis

Main Analysis Function for GLOSSA Package
pa_optimal_cutoff

Optimal Cutoff for Presence-Absence Prediction
predict_bart

Make Predictions Using a BART Model
generate_pseudo_absences

Generate Pseudo-Absence Points Using Different Methods Based on Presence Points, Covariates, and Study Area Polygon
plot_cv_folds_points

Plot cross-validation fold assignments
glossa_export

Export Glossa Model Results
plot_cv_metrics

Plot cross-validation metrics
misClassError

Misclassification Error
optimalCutoff

Compute the optimal probability cutoff score
remove_duplicate_points

Remove Duplicated Points from a Dataframe
remove_points_polygon

Remove Points Inside or Outside a Polygon
layer_mask

Apply Polygon Mask to Raster Layers
validate_fit_projection_layers

Validate Fit and Projection Layers
get_covariate_names

Get Covariate Names
specificity

Calculate the specificity for a given logit model
validate_layers_zip

Validate Layers Zip
sparkvalueBox

Create a Sparkline Value Box
response_curve_bart

Calculate Response Curve Using BART Model
run_glossa

Run GLOSSA Shiny App
read_presences_absences_csv

Read and validate presences/absences CSV file
read_extent_polygon

Read and Validate Extent Polygon
sensitivity

Calculate the sensitivity for a given logit model
variable_importance

Variable Importance in BART Model
validate_pa_fit_time

Validate Match Between Presence/Absence Files and Fit Layers
youdensIndex

Calculate Youden's index
read_layers_zip

Load Covariate Layers from ZIP Files
generate_cv_folds

Generate cross-validation folds
fit_bart_model

Fit a BART Model Using Environmental Covariate Layers
clean_coordinates

Clean Coordinates of Presence/Absence Data
buffer_polygon

Enlarge/Buffer a Polygon
extract_noNA_cov_values

Extract Non-NA Covariate Values
generate_pa_buffer_out

Generate Pseudo-Absences Using Buffer-Out Strategy
export_plot_ui

Create UI for Export Plot Button
evaluation_metrics

Evaluation metrics for model predictions
export_plot_server

Server Logic for Export Plot Functionality
cross_validate_model

Cross-validation for BART model
downloadActionButton

Create a Download Action Button
create_coords_layer

Create Geographic Coordinate Layers
contBoyce

Continuous Boyce Index (CBI) with weighting