Marine Protected Area Shapefiles - EU and non-EU MPAs

R workflow to harmonize and merge multiple MPA datasets, resolve overlapping protection polygons by priority, and generate regional marine-only shapefiles for EU and non-EU waters.

The project combines source data from EU, UK, Iceland, and WDPA-derived layers, then outputs cleaned, de-overlapped MPA polygons for key regions (Mediterranean, Baltic, Black Sea, and NE Atlantic including UK).

Outputs will be used in WP4 of the B-USEFUL project to assess the spatial match or mismatch between biodiversity hotspots and current marine protection in Europe, and its implications for biodiversity management.

Purpose

• Harmonize heterogeneous MPA attributes into a single schema.
• Merge and validate polygon geometries across source datasets.
• Resolve overlaps by retaining the highest protection level.
• Export marine-only regional shapefiles ready for downstream analyses.

Methods and Workflow

1. Download published data bundle from Zenodo (0_Download_Inputs_Outputs_from_Zenodo.R).
2. Merge and standardize source MPAs (EU, UK, Iceland, Albania, Greenland) into one layer (1_Merge_MPA_shapefiles.R).
3. Intersect, de-overlap, and marine-clip by protection priority using robust geometry rebuild, masking, and the safe intersection helper sourced within 2_Intersect_MPA_polygons.r (helper: safe_intersection.r).
4. Export shapefile + zip archive for the selected region (configured in export_name inside script 2).
5. Generate figure outputs (map + circular proportion panel) with 3_Multipanel_map_Protection_level_surface.R.

Note: If you download Outputs.zip from Zenodo, you can run script 3 directly to generate figures. In that case, scripts 1 and 2 do not need to be run.

Inputs and Data

• Zenodo record:
• Published archives:
  • Inputs.zip
  • Outputs.zip
• Main input folder: Inputs/
  • EU source data (Aminian-Biquet et al. 2024), DOI: 10.1016/j.dib.2024.111177
  • UK source data (Figshare package), DOI: 10.6084/m9.figshare.29901479
  • Iceland revised protection layer
  • WDPA-based Albania and Greenland layers. UNEP-WCMC and IUCN (2025), Protected Planet: The World Database on Protected Areas (WDPA) [On-line], December 2025, Cambridge, UK: UNEP-WCMC and IUCN. Available at: www.protectedplanet.net
  • IHO world seas polygons used for marine clipping. Flanders Marine Institute (2018). IHO Sea Areas, version 3. Available online at marineregions.org. DOI: 10.14284/323

Outputs

• Intermediate merged object: Outputs/shp_mpa_europe_all.rda
• Regional final outputs (shapefile directories and optional .zip exports), e.g.:
  • Outputs/shp_mpa_med_sea
  • Outputs/shp_mpa_black_sea
  • Outputs/shp_mpa_baltic_sea
  • Outputs/shp_mpa_NE_Atlantic_incl_UK

Figures

• Figure outputs are saved in a separate Figures/ folder, including:
  • Figures/Map_multipanel_Protection_level_all_with_circular_proportion.png

Installation and Environment

• R version: 4.2.2
• Core packages: sf, dplyr, lwgeom, readxl, zenodor, ggplot2, patchwork, rnaturalearth
• Zenodo helper package: 0_Download_Inputs_Outputs_from_Zenodo.R auto-installs zenodor from GitHub (FRBCesab/zenodor) if missing.

Basic Usage

1. Download or refresh Inputs/ and Outputs/ from Zenodo:

   source("0_Download_Inputs_Outputs_from_Zenodo.R")

2. Build harmonized all-Europe MPA object:

   source("1_Merge_MPA_shapefiles.R")

3. Generate one regional de-overlapped output (configure region + export_name in script):

   source("2_Intersect_MPA_polygons.r")

4. Generate the combined map + circular proportion figure:

source("3_Multipanel_map_Protection_level_surface.R")

If Outputs/ comes from the Zenodo archive and already contains the required regional shapefiles, you can skip steps 2 and 3 and run only step 4 for figure generation.

Repository Structure

• 0_Download_Inputs_Outputs_from_Zenodo.R: Download/unzip Inputs.zip and Outputs.zip from Zenodo.
• 1_Merge_MPA_shapefiles.R: Standardize and merge source MPA datasets.
• 2_Intersect_MPA_polygons.r: Priority-based de-overlap, marine clipping, and export.
• 3_Multipanel_map_Protection_level_surface.R: Generates the Europe map and combined map + circular protection-surface proportion figure.
• safe_intersection.r: Safe geometry intersection utility with repair fallback, called from script 2.
• Inputs/: Source spatial data (typically git-ignored in local workflows).
• Outputs/: Generated products and exported shapefiles.
• Figures/: Saved plot outputs (maps and summary figures from script 3).

Citation

If you use this code or dataset, please cite:

• Dataset: Moullec, F. (2026). Marine Protected Area Shapefiles - EU and non-EU MPAs (Version V1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.18701898
• Code: This GitHub repository (MoullecF/EU_MPA_B_USEFUL).
• B-USEFUL Deliverable 4.3: ADD WEB LINK of the report.

License

• Data license: Creative Commons Attribution 4.0 International (CC BY 4.0), as provided on Zenodo.