Quantifying year-round nocturnal bird migration with a fluid dynamics model.

Raphaël Nussbaumer^1,2 , Lionel Benoit² , Grégoire Mariethoz² , Felix Liechti¹ , Silke Bauer¹ and Baptiste Schmid¹

¹Swiss Ornithological Institute, Sempach, Switzerland, ²Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland

Corresponding author: Raphaël Nussbaumer (raphael.nussbaumer@vogelwarte.ch)

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Ouput:

• Publication in J. R. Soc. Interface <div data-badge-popover="right" data-badge-type="1" data-doi="10.1098/rsif.2021.0194" data-condensed="true" data-hide-no-mentions="true" class="altmetric-embed"></div>
• Visualization of the interpolation.
• BioRxiv Preprint <div data-badge-popover="right" data-badge-type="1" data-doi="10.1101/2020.10.13.321844" data-condensed="true" data-hide-no-mentions="true" class="altmetric-embed"></div>

Data Pre-processing

These scripts perform the pre-processing explained in the Supplementary Material 1.

1. Download and cleaning (script_download_cleaning.m)
   • L3-L10: Download all data available on enram repository for the entire year of 2018.
   • L50-L76: Delete the data of all radar with aparrent error in them
   • L97-L118: Reshape data to be on a regular grid: 5min interval, same altitudinal bins.
   • L120-L158: Compute sunrise and sunset at each radar location
   • L248-L278: Manually clean the data (use a MATLAB app CleaningV.mlapp)
   • L281-L346: More automatic post-cleaning processing: removal of single data point isolated by 30min. Noise removal (replace value exeeding twice the average of 8 surounding values by the mean of the surounding values), interpolate to 5000m.
   • L439-L488: Cleaning of flight speed componenet and sd_vvp based on the clearning performed on density.
2. Correction for elevation (script_elevation_correction.m)
   • L91-L170: MPS simulation for the lower elevation
   • L231-L381: Compute volume available for flight

The final vertial profile of bird density and flight speed vector can also be downloaded from zenodo .

Interpolation

These scripts perform the interpolation explained in the Supplementary Material 2. See each livescript for more information.

1. Inference of bird density Density_inference.mlx
2. Interpolation of bird density Density_estimationMap.mlx
3. Inference of flight speed Flight_inference.mlx
4. Interpolation of flight speed Flight_estimationMap.mlx
5. Simulation of bird densityDensity_simulation.m

Flow Model

• Flow model for the estimation map SinkSource.mlx
• Flow model for the simulations map SinkSourceSimulation.mlx

These files contain both the code to compute the fluxes and also the figures of the paper.