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paper_markov

This repository implements the code used in the paper "Modelling optimal vaccination strategies against Covid-19 in a context of Gamma variant predominance in Brazil" by Ferreira et al.

Preprint

Repository structure

  • functions/ contains (most) the functions used to prepare data, simulate and plot the results. The important files are:

    • markov_all_vac.R: contains the model

    • epi_params_all_vac.R: contains the epidemiologic parameters and initial structuring of the model

    • vac_params_all_vac.R: contains the vaccination parameters of the model (but not really the effectiveness parameters)

    • sensitivity_analysis_C1_2.R: contains the actual distribution of parameters used in the results

    • SA_{coverage, ideal, deaths, production}.R: contains the script to generate the results in the model. Notice that these scripts run several samples of the model and might take a while to run. To avoid this, these scripts provide the lines to load the tabulated results.

    • run_all_vac.R: contains a simple script to plot a single result of the model

  • DATA/ contains the data used to structure the model, from age distribution to vaccine doses expected.

  • results/ contains the tabulated results.

  • plots/ contains the figures generated with the results

Important dependencies

Tested in Ubuntu 64-bits 20.04. R version 4.1.2 (but expect to work with version > 3.6).

Packages Tidyverse, Matrix and doParallel are used.