This repository contains code and data used in the project on a distance-dependent pattern of collective escape in flocks of pigeons:

Papadopoulou M, Hildenbrandt H, Sankey DWE, Portugal SJ, Hemelrijk CK (2022) Selforganization of collective escape in pigeon flocks. PLoS Comput Biol 18(1): e1009772. https://doi.org/10.1371/journal.pcbi.1009772

The code provided is open source, but we ask you to cite the above paper if you make use of it.

The computational model (in C++) used to produce the simulated data can be found here: https://github.com/marinapapa/HoPE-model . The analysis on empirical and simulated data is performed in R, version 3.6 or later. See DESCRIPTION for details on depedencies.

• Files that reproduce the respective figures of the manuscript: figX.R
• Files with helper functions for analysis and ploting: count_switch_esc_dir.R, load_data.R, neighb_rel_pos.R, prepare_sim_data_for_turn_dir.R, subplots_functions.R
• Files for statistical analysis: analyze_empirical.R, analyze_turn_direction_trend.R

You can download all data from this Zenodo repository: https://zenodo.org/record/4993109

To smoothly run the code files, the subdirectories of the downloaded data should be copied locally in this Data folder. The dataset includes:

Empirical data: collected and preprocessed by Daniel W. E. Sankey, first published in:
Sankey DWE, Storms RF, Musters RJ, Russell WT, Hemelrijk CK, Portugal SJ. (2021) Absence of “selfish herd” dynamics in bird flocks under threat. Current Biology. https://doi.org/10.1016/j.cub.2021.05.009. They comprise analysed GPS tragectories of flocks of homing pigeons.

Simulated data: extracted by the computational model HoPE (Homing Pigeons Escape), an agent-based model adjusted to the collective escape of homing pigeons.

The files/folders necessary for the code to run are:

1. turning_direction folder in the empirical folder: contains the empirical data from the analysis on turning direction frequency
2. transformed folder in the empirical folder: contains the empirical data of Sankey et al. (2021) restructured according to the output of the computational model
3. HoPE_track_eg folder in the simulated_raw folder: an example output folder that is also used in Figure 6. The repository contains also all the raw output of all our experiments.
4. turning_direction in the simulated folder: the results of the turning direction frequency analysis on the simulated data
5. & 6. sim_datas_chase.RData and sim_datas_noavoid.RData in the simulated folder: the imported data from our main simulations.

Folder in which figX.R scripts export the figures.

• For any issue or more information on this repository, email Marina Papadopoulou at: [email protected]