phage_competition_paper_frontiers

Repository of bare minimum code needed for some of the simulations done in the paper submitted to Frontiers. They will need to be modified for running against multiple parameters

Using the scripts:

1. Python Script paper_payoff_matrix.py: Integrates the default phage-bacteria ODE system across all combinations of fixed lysogeny propensity and writes the output to a file which is used by the MATLAB script. Users can change the parameter set and initial conditions. This refers to the main text section: 'Methods > Game theoretic formulation to find the "optimal" lysogeny propensity.'

2. MATLAB script payoff_maker.m: Can open the file generated by the Python script paper_payoff_matrix.py and generate the payoff matrix for all lysogeny propensities of both phages. It also finds the mini-max point on the payoff surface which gives us the optimal fixed lysogenic propensity. This refers to the main text section: 'Methods > Game theoretic formulation to find the "optimal" lysogeny propensity.'

3. Python script paper_script_moi.py: Runs the simulated evolution game as mentioned in the main text section: 'Methods > Including Multiple Infections in the Model'

4. C++ code infectedBacteriaCoarse_phageCompetition.cpp: Runs a spatial model of the phage bacteria system as mentioned in the supplemental material section 'Spatial Model'