Appendix A — Resources

A.1 Forum

If you are actively using the package, join the GeoPressure forum to stay informed about bugs, issues, and improvements.

A.2 Main Publications

Main paper presenting the approach to estimate a likelihood map from pressure timeseries:

Nussbaumer, R., Gravey, M., Briedis, M., & Liechti, F. (2023). Global positioning with animal-borne pressure sensors. Methods in Ecology and Evolution, 14, 1104–1117. https://doi.org/10.1111/2041-210X.14043

Paper presenting the movement model:

Nussbaumer, R., Gravey, M., Briedis, M., Liechti, F. & Sheldon, D. (2023) Reconstructing bird trajectories from pressure and wind data using a highly optimised hidden Markov model. Methods in Ecology and Evolution, 14, 1118–1129. https://doi.org/10.1111/2041-210X.14082

Paper reviewing the strengths, limitations, and opportunities of geolocation by pressure from a more applied perspective:

Rhyne, G. S., Stouffer P. C., Briedis, M., Nussbaumer, R. (2024). Barometric geolocators can reveal unprecedented details about the migratory ecology of small birds. Ornithology. https://doi.org/10.1093/ornithology/ukae010

A.3 Presentations

Raphaël Nussbaumer. GeoPressureR: Introduction and case studies. August 2023. 14th European Ornithologicals’ Union Congress. PRESENTATION available as PDF.

Raphaël Nussbaumer, Colin Jackson, Lennox Kirao, Felix Liechti. The potential of multi-sensor geolocators to study short-distance Afrotropical migrants. November 2022. 15th Pan-African Ornithological Congress. PRESENTATION available as PDF.

Raphaël Nussbaumer, Mathieu Gravey, Martins Briedis, Felix Liechti. Leveraging light, pressure, activity, and wind data to improve geolocator positioning. August 2022. 28th International Ornithological Congress. PRESENTATION available at Youtube and as PDF.

Raphaël Nussbaumer, Mathieu Gravey, Felix Liechti. Improving the spatial accuracy of multi-sensor geolocators’ position using atmospheric surface pressure. October 2021. 7th International Bio-logging Science Symposium. PRESENTATION available at Youtube and as PDF.

A.4 Map tiles

Interactive GeoPressureR maps use a basemap to provide geographic context. GeoPressureViz, GeoLightViz, plot() maps, and plot_path() all show the same basemap selector.

Esri’s Gray Canvas, imagery, and topographic basemaps are always available. You can add CARTO, Mapbox, or MapTiler styles by storing a provider key once in your system keyring.

keyring::key_set_with_value("CARTO_API_KEY", password = "<your CARTO API key>")
keyring::key_set_with_value("MAPBOX_ACCESS_TOKEN", password = "<your Mapbox token>")
keyring::key_set_with_value("MAPTILER_API_KEY", password = "<your MapTiler API key>")

Only store a public, read-only Mapbox token: rendered Leaflet maps send map tokens to the web browser. Do not put keys in analysis scripts or commit them to version control. Create keys at CARTO, Mapbox, or MapTiler.

Each configured provider adds useful styles to the selector: CARTO Dark Matter with and without labels; Mapbox Dark, Outdoors, Satellite, and Satellite Streets; and MapTiler DataViz Dark, Topographic, Satellite, and Hybrid. Choose a dark no-label layer for likelihood maps, a topographic layer for terrain context, and satellite or hybrid imagery for local detail.

A.5 References

Allard, Denis, A. Comunian, and Philippe Renard. 2012. “Probability Aggregation Methods in Geoscience.” Mathematical Geosciences 44 (July): 545–81. https://doi.org/10.1007/s11004-012-9396-3.

Basson, Marinelle, Mark V. Bravington, Jason R. Hartog, and Toby A. Patterson. 2016. “Experimentally Derived Likelihoods for Light-Based Geolocation.” Methods in Ecology and Evolution 7 (August): 980–89. https://doi.org/10.1111/2041-210X.12555.

Bindoff, Aidan D., Simon J. Wotherspoon, Christophe Guinet, and Mark A. Hindell. 2018. “Twilight‐free Geolocation from Noisy Light Data.” Methods in Ecology and Evolution 9 (May): 1190–98. https://doi.org/10.1111/2041-210X.12953.

Copernicus Climate Change Service. 2018. ERA5 Hourly Data on Pressure Levels from 1940 to Present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS). https://doi.org/10.24381/CDS.BD0915C6.

Copernicus Climate Change Service. 2019. ERA5-Land Hourly Data from 1950 to Present. Copernicus Climate Change Service (C3S) Climate Data Store (CDS). https://doi.org/10.24381/CDS.E2161BAC.

Lisovski, Simeon, Silke Bauer, Martins Briedis, et al. 2020. “Light‐level Geolocator Analyses: A User’s Guide.” Journal of Animal Ecology 89 (January): 221–36. https://doi.org/10.1111/1365-2656.13036.

Nussbaumer, Raphaël, Mathieu Gravey, Martins Briedis, and Felix Liechti. 2023. “Global Positioning with Animal‐borne Pressure Sensors.” Methods in Ecology and Evolution 14 (4): 1104–17. https://doi.org/10.1111/2041-210X.14043.

Nussbaumer, Raphaël, Mathieu Gravey, Martins Briedis, Felix Liechti, and Daniel Sheldon. 2023. “Reconstructing Bird Trajectories from Pressure and Wind Data Using a Highly Optimized Hidden Markov Model.” Methods in Ecology and Evolution 14 (4): 1118–29. https://doi.org/10.1111/2041-210X.14082.

Patterson, Toby A., Len Thomas, Chris Wilcox, Otso Ovaskainen, and Jason Matthiopoulos. 2008. “State-Space Models of Individual Animal Movement.” Trends in Ecology and Evolution 23 (2): 87–94. https://doi.org/10.1016/j.tree.2007.10.009.

Tobias, Joseph A., Catherine Sheard, Alex L. Pigot, et al. 2022. “AVONET: Morphological, Ecological and Geographical Data for All Birds.” Ecology Letters 25 (3): 581–97. https://doi.org/10.1111/ele.13898.