Repository of the "Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant" code

README

This repository provides the script to reproduce the fitting analysis and figures from Coutinho et al. 2021

Notes:

• This code runs best on R version 4.0.3 or above.
• The code is also optimized for [linux].
• When you first run the code from Run_analysis.R, R will install all required packages.
• Running all.params.exploration() and fit_minima() takes a large number of hours to complete. For convenience, we also provide the tables resulting from these function as .csv files.

Run the file Run_analysis.R to reproduce the paper`s main analysis and sensitivity analysis.

The following values correspond to the parameters presented in Table 1:

• REL.BETA.RATE2: Relative transmission rate for the new variant
• PROB.REINFEC.V2: Relative force of reinfection of P.1
• prevalence: Prevalence of previous infection (2020-11-01) (%)
• INIT.V2.FRAC: Initial fraction of the new variant (2020-11-01)
• r: Intrinsic growth rate
• IHR.V2.PROP: odds ratio of P.1 parameters relative to wild variant

References:

Coutinho, R. M., Marquitti, F. M. D., Ferreira, L. S., Borges, M. E., da Silva, R. L. P., Canton, O., … & Prado, P. I. (2021). Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P. 1 variant. medRxiv.