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

Raphaël Nussbaumer1,2 , 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)


Ouput:

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 DOI.

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

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