This repository is a bit chaotic, as the project has become a multi-year effort and my programming/organizational skills have evolved along with it. I used Python and Jupyter notebooks to do analysis and plotting. There is an implementation of the simulator in C++ that must be built into a Python module in order for the notebooks to run.
The main external dependencies are NumPy,
pandas,
Plotly, and
Jupyter. My environment contains
plotly==3.3.0 and Python 3.6.4. Newer versions of Plotly may break things.
- Make sure NumPy is installed in your environment.
- Inside
simulator-cpp, runpython setup.py build. - Run
python setup.py install, or move the resulting.pydor.sofrom thebuild/lib.systemdirectory intonotebooks-py. - Use Jupyter Notebook or JupyterLab to view the notebooks in
notebooks-py.
- Ogbunugafor, C., Eppstein, M. Competition along trajectories governs adaptation rates towards antimicrobial resistance. Nat Ecol Evol 1, 0007 (2017). https://doi.org/10.1038/s41559-016-0007
- Mira, P. M. et al. Rational Design of Antibiotic Treatment Plans: A Treatment Strategy for Managing Evolution and Reversing Resistance. PLOS ONE 10, e0122283 (2015). https://doi.org/10.1371/journal.pone.0122283