This repository provides the R code that accompanies the article:
March, D, Boehme, L, Tintoré, J, Vélez‐Belchi, PJ, Godley, BJ. Towards the integration of animal‐borne instruments into global ocean observing systems. Glob Change Biol. 2019; 00: 1– 11. https://doi.org/10.1111/gcb.14902
- R-studio with R >= 3.1.0
- Packages:
- Data manipulation: dplyr, lubridate, stringr, reshape2, data.table, foreign, Hmisc
- Spatial data: rgdal, maptools, geosphere, rgeos, sp, raster, ncdf4
- Plots: ggplot2
- API: rfishbase, rredlist, jsonlite
The R code can be downloaded from the following link. Additionaly, check out this guideline at the Rstudio website for installing Git on your computer and creating a new project.
There several steps that need to be conducted before running the scripts.
- Download raw data from third-party providers (see bellow)
- Edit the paths to those datasets
- Run the scripts following the suggested order from folders and scripts
Most of the data used is open and freely available. However, some datasets (e.g. Birdlife, SWOT and OBIS-SEAMAP) will require a data request or form registration with the data providers.
- The GEBCO 2014 Grid, version 20150318, www.gebco.net.
- Land polygons using the 1:50 vector map from Natural Earth (www.naturalearthdata.com),
- SeaVox Salt and Fresh Water Body Gazetter (v16 2015) from Marine Regions (http://www.marineregions.org)
- Exclusive Economic Zones (EEZ) from Marine Regions (http://www.marineregions.org).
- Profile directory of Argo floats. Argo (2000). Argo float data and metadata from Global Data Assembly Centre (Argo GDAC). SEANOE. http://doi.org/10.17882/42182.
- IUCN. The IUCN Red List of Threatened Species. Version 2017-3. http://www.iucnredlist.org. (2017).
- MEOP-CTD database. http://doi.org/10.17882/45461
- OBIS-SEAMAP. Halpin, P. et al. OBIS-SEAMAP: The World Data Center for Marine Mammal, Sea Bird, and Sea Turtle Distributions. Oceanography 22, 104–115 (2009).
- BirdLife International and Handbook of the Birds of the World (2017) Bird species distribution maps of the world. Version 2017.2. Available at http://datazone.birdlife.org/species/requestdis.
- SWOT. Kot, C. Y. et al. The State of the World’s Sea Turtles Online Database: Data provided by the SWOT Team and hosted on OBIS-SEAMAP. Oceanic Society, Conservation International, IUCN Marine Turtle Specialist Group (MTSG), and Marine Geospatial Ecology Lab, Duke University. Available at: http://seamap.env.duke.edu/swot.
This project uses an external service IUCN that requires the generation of a token. It also uses the API from FishBase and SeaLifeBase.
Distribution ranges of seabirds were provided in a ESRI geodatabase by Birdlife . Previous to link them with the species list, a filtered query was constructed using ArcMap software. Further details are provided in the script 05_link_eoo.R
Copyright (c) 2019 David March
Licensed under the MIT license.
March, D, Boehme, L, Tintoré, J, Vélez‐Belchi, PJ, Godley, BJ. Towards the integration of animal‐borne instruments into global ocean observing systems. Glob Change Biol. 2019; 00: 1– 11. https://doi.org/10.1111/gcb.14902
We gratefully acknowledge funding by the BBVA Foundation (“Ayudas Fundación BBVA a Equipos de Investigación Científica 2016”) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 794938. DM acknowledge support from Spanish Government (grant “Juan de la Cierva-Formación” FJCI-2014-20064, grant “José Castillejo” CAS17/00193). We thank all the data providers for making their data available and making this study possible.