This repo contains the workflows to generate emerging trends for Europe's Large Marine Ecosystems. Such workflows are based on species occurrence cubes, a concept developed during the TrIAS project and made operational by GBIF and the B-Cubed project.
The emerging trends indicators calculated in this repository have been conceived and applied at Belgian and regional level during the TrIAS project, see occurrence-based indicators.
├── src/
│ ├── assign_grid_cells_to_lme.R # Assigns EEA 10×10 km grid cells to Large Marine Ecosystems (LMEs)
│ ├── calculate_indicators.R # Downloads the latest species occurrence cube and calculates emerging-trend indicators per LME
│ └── utils.R # Shared utility functions used by the scripts above
├── data/
│ ├── input/ # Species occurrence cubes downloaded from GBIF (CSV files)
│ └── output/
│ ├── grid_cells_with_lme_info.csv # Mapping of EEA grid cell codes to LME identifiers
│ ├── last_cube_key.csv # GBIF download key of the most recently processed occurrence cube
│ ├── emerging_species_lme_combinations.csv # Species × LME combinations with an emerging trend
│ ├── emerging_trends_summary.csv # Per-species/LME emerging-trend classification and statistics
│ ├── emerging_trends_ranking_list.csv # Ranked list of emerging species per LME
│ ├── appearing_species.csv # Species newly appearing in an LME
│ ├── reappearing_species.csv # Species reappearing in an LME after absence
│ └── indicators_plots/ # Indicator plots per species and LME
│ ├── *.zip # Zip archives of plots per LME
│ └── png/ # Individual PNG plots per species and LME
├── .github/
│ └── workflows/
│ └── calculate-indicators-and-create-pr.yml # GitHub Actions workflow that runs the full pipeline and opens a PR with the results
├── DESCRIPTION # R package metadata (title, version, authors, dependencies)
├── LICENSE
└── LICENSE.md
This work is being developed in the framework of the GuardIAS project. GuardIAS receives funding from the European Union’s Horizon Europe Research and Innovation Programme (ID No 101181413).