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.
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functions/ contains (most) the functions used to prepare data, simulate and plot the results. The important files are:
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markov_all_vac.R: contains the model
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epi_params_all_vac.R: contains the epidemiologic parameters and initial structuring of the model
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vac_params_all_vac.R: contains the vaccination parameters of the model (but not really the effectiveness parameters)
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sensitivity_analysis_C1_2.R: contains the actual distribution of parameters used in the results
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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.
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run_all_vac.R: contains a simple script to plot a single result of the model
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DATA/ contains the data used to structure the model, from age distribution to vaccine doses expected.
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results/ contains the tabulated results.
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plots/ contains the figures generated with the results
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.