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Bird tracking

This repository contains the functionality to standardize data from the LifeWatch GPS tracking network for large birds so these can be published on Movebank.

Workflow

UvA-BiTS

  • Reference data: UvA-BiTS database β†’ Script to query data in the Movebank data format (defined in SQL) β†’ Generated file that can be uploaded to Movebank
  • GPS data: same as reference data
  • Accerelation data: same as reference data

Ornitela

  • Reference data: Spreadsheet β†’ Script to query data in the Movebank data format (defined as dplyr::mutate()) β†’ Generated file that can be uploaded to Movebank
  • GPS data: Ornitela database β†’ Live feed to Movebank by associating a selection of tags to a study
  • Acceleration data: not yet defined

Datasets

Movebank & Zenodo

Title Movebank Zenodo Status
BOP_RODENT - Rodent specialized birds of prey (Circus, Asio, Buteo) in Flanders (Belgium) 1278021460 active
DELTATRACK - Herring gulls (Larus argentatus, Laridae) and Lesser black-backed gulls (Larus fuscus, Laridae) breeding at Neeltje Jans (Netherlands) 1258895879 active
H_GRONINGEN - Western marsh harriers (Circus aeruginosus, Accipitridae) breeding in Groningen (the Netherlands) 922263102 DOI stopped in 2018, described in Milotic et al. 2020
HG_OOSTENDE - Herring gulls (Larus argentatus, Laridae) breeding at the southern North Sea coast (Belgium) 986040562 DOI active
LBBG_JUVENILE - Juvenile lesser black-backed gulls (Larus fuscus, Laridae) hatched in Zeebrugge (Belgium) 1259686571 active
LBBG_ZEEBRUGGE - Lesser black-backed gulls (Larus fuscus, Laridae) breeding at the southern North Sea coast (Belgium and the Netherlands) 985143423 DOI active
MH_ANTWERPEN - Western marsh harriers (Circus aeruginosus, Accipitridae) breeding near Antwerp (Belgium) 938783961 DOI active, described in Milotic et al. 2020
MH_WATERLAND - Western marsh harriers (Circus aeruginosus, Accipitridae) breeding near the Belgium-Netherlands border 604806671 DOI stopped in 2018, described in Milotic et al. 2020
O_WESTERSCHELDE - Eurasian oystercatchers (Haematopus ostralegus, Haematopodidae) breeding in East Flanders (Belgium) 1099562810 DOI active

Steps to upload data to Zenodo are described here.

GBIF

Title Β GBIF Β Remark
Bird tracking - GPS tracking of Lesser Black-backed Gulls and Herring Gulls breeding at the southern North Sea coast Β DOI Subset of HG_OOSTENDE and LBBG_ZEEBRUGGE, described in Stienen et al. 2016
Bird tracking - GPS tracking of Western Marsh Harriers breeding near the Belgium-Netherlands border DOI Β Subset of MH_WATERLAND

Repo structure

The repository structure is based on Cookiecutter Data Science. Files and directories indicated with GENERATED should not be edited manually, those with IGNORED are ignored by git and will not appear on GitHub, and those with DEPRECATED are no longer maintained.

β”œβ”€β”€ README.md           : Description of this repository
β”œβ”€β”€ LICENSE             : Repository license
β”œβ”€β”€ bird-tracking.Rproj : RStudio project file
β”œβ”€β”€ .gitignore          : Files and directories to be ignored by git
β”‚
β”œβ”€β”€ cartodb             : Documentation for gps tracking data on CartoDB, see
|                         https://inbo.carto.com/u/lifewatch/ DEPRECATED
|
β”œβ”€β”€ explorer            : Source code for an online exploratory tool, see 
|                         https://oscibio.inbo.be/blog/bird-tracking-explorer/ DEPRECATED
|
β”œβ”€β”€ src
β”‚   β”œβ”€β”€ functions       : Custom functions used in scripts
β”‚   β”œβ”€β”€ movebank_ornitela.Rmd : Script to get data for a specific Ornitela project in Movebank format
β”‚   β”œβ”€β”€ movebank_uvabits.Rmd : Script to get data for a specific UvA-BiTS project in Movebank format
β”‚   └── outliers.Rmd    : Script to mark outliers based on high speeds
β”‚
β”œβ”€β”€ sql
β”‚   β”œβ”€β”€ movebank_ref.sql: Query to get reference data in Movebank format
β”‚   β”œβ”€β”€ movebank_gps.sql: Query to get gps data in Movebank format
β”‚   └── movebank_acc.sql: Query to get acceleration data in Movebank format
β”‚
└── data
    └── processed       : Data that can be uploaded to Movebank GENERATED IGNORED (reference data is versioned)

Contributors

List of contributors

License

MIT License