Movement decisions by black-tailed godwit families with chicks in an intensively managed dairy farming landscape

This repository contains the complete R workflow for analysing post-hatch movement, space use, and habitat selection of Black-tailed Godwit (Limosa limosa limosa) families in southwest Friesland (The Netherlands).

The workflow mirrors the structure of the associated manuscript. Scripts are numbered and organised by method section.

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Workflow

• clean and standardise multi-year GPS tracking data
• link tracking data to nest locations and natal meadows
• quantify post-hatch movement and space use
• assess selection for grassland management packages and grassland production intensity (GPI)
• generate manuscript figures and statistical outputs

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Scripts

Scripts are ordered numerically to reflect the analytical pipeline.

2.2 Tracking data collection and processing

• 1.filter_tracking_data.R
  Speed and spatial filtering of locations
• 2.clean_post_hatch_data.R
  Merge tracking data with family and nest metadata
• 3.crawl.R
  Regularise tracks to 6-hour intervals using CRAWL

2.3 Grassland management variables

• 1.process_management_packages.R
  Harmonise management categories, add protected sites, and create a complete management layer

2.4 Movement analyses

2.4.1 Space use estimation

• 1.annotate_natal_locations.R
  Assign natal meadow IDs and natal-location flags
• 2.quantify_parcels_visited.R
  Calculate number of unique parcels visited
• 3.daily_home_ranges.R
  Compute cumulative daily home ranges and summary statistics

2.4.2 Natal site importance

• 4.natal_site_importance

2.4.3 Effects of management strategies on habitat selection

• 5.nest_buffers.R
  Create nest-centred buffers (100–1,000 m)
• 6.rsf_gpi.R
  Resource selection for GPI with natal-location interaction
• 7.rsf_management.R
  Resource selection for management packages

Figures

• fig1.R, fig2.R, fig3.R, fig4.R, fig5.R, figS2.2.R,figS3.1.R,figS4.1.R

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Data description

Raw data (data/raw/)

• raw_locations.rds - raw GPS tracking data
• family_data.xlsx - Nest, hatch, and fledging metadata
• original_management.gpkg - Original grassland management scheme polygons
• protected_sites.gpkg - Protected area polygons
• swf_geometry.gpkg - Meadow parcel geometry for southwest Friesland
• gpi.gpkg – grassland production intensity polygons

Processed data (data/processed/)

Generated by scripts in this repository:

• all_parcels_visited_daily.rds - unique parcels visited per track id per day
• all_parcels_visited_yearly.rds - unique parcels visited per track id per year
• daily_home_ranges.gpkg – cumulative daily home ranges
• donut_buffers/ - donut-ring buffers (core + 100 m rings) with mean annual gpi values
• final_management.gpkg – harmonised management categories
• GPI_rasters/ - parcel level GPI rasters
• home_range_stats – per-track summary statistics
• KDE.gpkg - KDE home ranges for vizualizing movement in Figure 1
• locations_natal_annotated.rds - gps locations with natal flag
• natal_area_models/ - GLMM model objects
• nests.rds – nest point locations
• nest_buffers.rds – nest-centred buffers (100–1,000 m)
• post_hatch_data.rds - cleaned tracking dataset
• post_hatch_data_cleaned.rds – filtered post-hatch tracking data
• QGIS/ - individual tracks after manual foraging/roost site removal in QGIS
• rsf_model_500m.rds, rsf_model_1km.rds – fitted RSF models
• tracks_crawled.rds – regularised GPS tracks (6-hour interval)