Reproducible R workflow to (1) build species distribution products for Black Sea fishes from multi-source data, (2) aggregate outputs to a common grid, and (3) compute and analyze taxonomic, functional, and phylogenetic diversity patterns by bioregion.
Developed as part of an IMBRSea M.Sc. thesis project (2023) in the Modelling for Aquatic Systems (MAST) group (University of Liège).
- Builds depth-constrained species range polygons from occurrence records with bias-aware preprocessing and bathymetry constraints.
- Integrates complementary distribution sources when available (e.g., IUCN/FAO layers; fisheries-derived proxies).
- Aggregates final distributions to a 0.1° × 0.1° grid to generate a presence/absence community matrix.
- Computes taxonomic, functional, and phylogenetic diversity indices and produces maps/figures summarizing spatial patterns across Black Sea bioregions.
Scripts/— main workflow scripts (Part 1–3) and supporting functionsRasters/— intermediate raster layers / gridsMAYER_MasterThesis.Rproj— RStudio project
- Open
MAYER_MasterThesis.Rprojin RStudio. - Run the workflow scripts in
Scripts/in order:Master_part1— distribution/range products (multi-source mapping workflow)Master_part2— functional and phylogenetic indicesMaster_part3— statistical analyses and figure generation
This workflow draws on open biodiversity and fisheries sources (e.g., GBIF/OBIS occurrence data, IUCN/FAO distribution layers when available, and fisheries datasets), plus environmental layers for spatial constraints/analysis.
API keys/credentials are not stored in this repository. If an API-backed source is used (e.g., IUCN Red List), set your key via environment variables (e.g., ~/.Renviron).
Mayer, S. (2023). Linking patterns in phylogeny, traits, and space for Black Sea fish (M.Sc. thesis, IMBRSea / University of Liège).
Stefanie Mayer (https://stefanieseas.wordpress.com/)