Run code on Binder:
Code and data to reproduce results in the paper:
Smith, M. L., Davidson, J. D., Wild, B., Dormagen, D. M., Landgraf, T., and Couzin, I. D. (2022). The dominant axes of lifetime behavioral variation in honey bees. Submitted
Main analysis files descriptions:
- 'Fig1-IndividualExampleTrajectory.ipynb', 'FigsMain-Beeday-and-Beelife.ipynb','FigSupp-CombMaps.ipynb': These contain all the plots and results in the paper, and can be run with the included data
- Data Usage Example.ipynb: Contains simple, short example for reading in data
Other files:
- beesgithub.yml, requirements.txt: Environment used for analysis, either to install with conda or pip
- beeday-opentsne-train-1.pklz: saving tSNE results so don't have to always recalculate
- datafunctions.py, definitions_2018.py, displayfunctions.py, all_cohorts.csv: Contain functions and definitions used in the analysis
- definitions_2019.py, all_cohorts_2019.csv, summary_experiments_2019.csv: Definitions and information for 2019 data
- 'Data processing - 1 - metrics and dataframes.ipynb', Data processing - 0 - database query.ipynb: Codes used to process data.
The folder 'data2018' contains results needed to reprocedure figures and results in the paper. Full dataset, including x-y trajectories and behavioral metrics calculated at different timescales (per-hour,per-5 minute, per-1 minute), is available at Zenodo: https://doi.org/10.5281/zenodo.6045859