nl-birdmap

This repository accompanies the manuscript:

Hoekstra, B., Kranstauber, B., Bradarić, M., De Groeve, J., Shinneman, S., Wijers, B. C., Leijnse, H., van Gasteren, H., Dokter, A. M., van Loon, E., & Shamoun-Baranes, J. (2025). Large-scale mapping of nocturnal bird migration to accelerate a nature-inclusive energy transition. Journal of Environmental Management, 395, 127753. https://doi.org/10.1016/j.jenvman.2025.127753

It contains the code and data necessary to reproduce the key analyses and figures.

Authors

Bart Hoekstra¹, Bart Kranstauber¹, Maja Bradarić¹, Johannes De Groeve¹, Stacy Shinneman¹, Berend C. Wijers¹, Hidde Leijnse³, Hans van Gasteren^1,4, Adriaan M. Dokter^1,2, Emiel van Loon¹, Judy Shamoun-Baranes¹

¹ Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, The Netherlands
² Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Rd, Ithaca, NY 14850, United States of America
³ R&D Observations and Data Technology, Royal Netherlands Meteorological Institute, De Bilt, The Netherlands
⁴ Royal Netherlands Air Force, P.O Box 8762, 4820 BB Breda, The Netherlands

Data package ready-to-use outputs

This repository contains a data package with processed outputs, in the folder datapackage/ Where the other data in this repository is primarily intended to reproduce the analyses, the datapackage/ folder contains the ready-to-use GIS products that are also shown in the manuscript.

The datapackage includes:

• Seasonal passage maps for spring and autumn (raster, 500 × 500 m resolution)
• Bird density maps for both seasons
• Raw (unsmoothed) maps of vertically integrated reflectivity
• A .geojson file with areas of uncertainty (ground clutter and beam blockage), which should always be used in conjunction with the rasters

These files represent the final outputs of the workflow and can be directly used for visualization, spatial analyses, or integration into other projects. Make sure to cite the paper when using these data products.

Structure of this repository

This repository is organized around three key scripts:

1. radar-profiles.Rmd: Derives flight altitudes from vertical profile radar data. Produces Figure 1 of the manuscript.
2. birdmap.Rmd: Contains the processing from identified peak nights to the peak night distributions of migratory birds across the Netherlands, and the subsequent analysis of wind power-bird migration tradeoffs. Produces figure 2 and 3 of the manuscript.
3. rbc_preprocessing.R: Performs computationally intensive pre-processing of radar data to correct for range bias. Best run independently before executing birdmap.Rmd.

Data

This repository contains all data needed as initial input data, or GIS data to recreate the figures. Unfortunately, given the large data volume of weather radar data, it is impractical to share this here, but the data is freely available via the KNMI open data portal and can be accessed via the new {getRad} R package. The analysis notebooks show how files should be structured for the analysis and the folder structure has been retained by adding empty .gitkeep files to this repository.

A short summary table with of input files, their contents and sources is listed below. All files are located in data and the respective subfolders. A dash indicated in the source column indicates the data is created for the purpose of this study.

Filename	Subfolder	Source	Contents	URL	Comment
vp_mtr_ordered_seasonal_day_ night_migration.csv		-	Ranked nightly migration activity across radars derived from vertical profiles of birds		Main input file for the study, also contains information on daytime migration
dhl.csv	beam_blockage	-	Beam blockage for Den Helder radar		Generated with beam-blockage/beamblockage.ipynb
hrw.csv	beam_blockage	-	Beam blockage for Herwijnen radar		Generated with beam-blockage/beamblockage.ipynb
NL_Beamblockage.geojson	gis	-	Beam blockage for Dutch radars converted to .geojson	Derived from above
manual_clutter.geojson	gis	-	Manually drawn areas affected by ground clutter		Only if not resolved by beam blockage procedure
NL_Clutter-500m-Buffer.geojson	gis	-	.geojson of identified clutter areas buffered by 500m
Netherlands-5km-Buffer.geojson	gis	-	.geojson with an outline of the Netherlands buffered by 500m
Netherlands.geojson	gis	-	.geojson with an outline of the Netherlands
Noord-Holland-10km-Buffer.geojson	gis	-	.geojson with an outline of the province of North-Holland bufffered by 10km
Noord-Holland.geojson	gis	-	.geojson with an outline of the province of North-Holland
Radars-100km-Buffer.geojson	gis	-	.geojson with the area enclosed within 100km from both Dutch weather radars
Radars.geojson	gis	-	.geojson with the locations from both Dutch weather radars
gemeenten.geojson	gis	CBS	.geojson with the Dutch municipalities	URL	Not in final version of manuscript
rivm_20250101_windturbines_ ashoogte.shp	gis	RIVM	Shapefile with turbine locations and dimension information	URL	Not in final version of manuscript
altitude_profiles_weatherradar.rds	profiles	-	Aggregated altitude profiles from both Dutch weather radars
altitude_profiles_weatherradar.sql	profiles	-	SQL Query to aggregate altitude profiles from both Dutch weather radars
RES_zoekgebieden_*	gis/RES/	Province of North-Holland	Shapefiles with information on the search areas/candidate sites for renewable energy developments	URL
NLD_power-density_100m.tif	gis	Global Wind Atlas	Wind power density @ 100m	URL	Data paper: 10.1175/BAMS-D-21-0075.1
vp_mtr_cum50_cl.csv		-	.csv export of vp_mtr_cum50_cl object containing scan screening outcomes