J. Cricelio Montesinos-López, Maria L. Daza–Torres, Yury E. García, César Herrera, C. Winston Bess, Marlene K. Wolfe, Alexandria B. Boehm, Heather N. Bischel, Miriam Nuño
This module consists in the following files:
Data data_ww_cases.csv
Codes Example_Estimation of COVID-19 PR from ww data.ipynb Notebook tutorial to estimate of PR from ww data
run_mcmc.py Main code: • Set all the parameters for the models • Load and processed data • Likelihood, priors for mcmc are defined • Compute Priors from the posterior distributions
plot_data.py
- plot_data() To plot Normalized wastewater data (N/PMMoV), number of COVID-19 tests conducted, and positive cases.
- plot_conc_pos_rate() To plot 7 day- trimmed average of WW data (Smoothed N/PMMoV) and daily PR.
save_mcmc.py save_output() This function is for running and saving the mcmc for each period. We just save the output.
plot_PR_predictions.py
- plot_beta() To plot the posterior distribution of the model’s parameters for a forecast period.
- plot_post() To plot the estimated PR for a forecast period.
- plot_post_wave_beta() To plot the posterior distribution of the model’s parameters for all periods.
- plot_post_wave() To plot the estimated PR for all periods.
plot_estimated_Rt.py
- plot_Rt() To plot the Rt from estimated PR using the algorithm of Cori et al 2013.
- plot_all_Rt()
To plot the Rt for all periods.
threshold.py
- FindClosestIndex() Find the index of the closest item (time, array) in tt to d[i] (ops. time)
- find_thresholds() Find the value of WW concentration, c, such that with probability alpha the positivity rate is less than or equal to the CDC threshold. plot_thresholds() To plot computed thresholds for all periods.
Auxiliary program: pytwalk.py Library for the t-walk MCMC algorithm. For more details about this library see https://www.cimat.mx/~jac/twalk/ Cori, A., Ferguson, N. M., Fraser, C., & Cauchemez, S. (2013). A new framework and software to estimate time-varying reproduction numbers during epidemics. American journal of epidemiology, 178(9), 1505-1512.