param4ramp-covid

Sensitivty analysis for Contact Tracing Model in RAMP COVID-19 Project.

Randomly generate samples of model parameters, and perform regression between the input parameters and output time-series of SEIR.

Requirement

numpy, scipy, pandas, scikit-learn, docopt, shap, matplotlib

Usage

uk.co.ramp.exec.draw_parameters is a command-line program to generate samples of model parameters and corresponding model output time-series. These samples should be fed into uk.co.ramp.exec.analyse_sensitivity to understand which parameter strongly affects which aspect of the output time-series.

Simply executing each script provides a list of command-line options.

python draw_parameters.py 
python analyse_sensitivity.py 

Example

Below you get ${HOME}/covid-19/resultrelative_importance.biased.csv and ${HOME}/covid-19/resultrelative_importance.unbiased.csv as the final results. These CSV files contain which parameter strongly affects the total number of severe infections and that of deaths over the entire simulation period. In the future the metrics we focus on can be customisable.

python draw_parameters.py ~/covid-19/result --n-simulations=1000 \
  --java-project-dir=~/git/Contact-Tracing-Model \
  --tmp-dir=~/covid-19/tmp
  
python analyse_sensitivity.py ~/covid-19/result ~/covid-19/result