CristanchoLina/HhSeroAfricaChainBin

Data and code for the article: "Assessing SARS-CoV-2 transmission in African households from the reanalysis of serosurveys" # HhSeroAfricaChainBin Data and code for the article: "Assessing SARS-CoV-2 transmission in African households from the reanalysis of serosurveys" - source: all the .R scripts that contain the functions needed to run the model: - utils_computegenerations: script to generate all possible combinations of generation sets for household of size 2-7. Generates sero_dat_combis.RData - sero_dat_combis.RData: contains all possible combinations of generation sets for household of size 2-7 - utils_formatdata.R: functions to format data for each study filtering according to given minhhsize, maxxhsize, maxNA. - utils_forstan_all_priormiss.R: wrapper R function to call .stan file for inference in real datasets (takes into account that the prior of seropositivity is not necessarily 50%) - utils_forstan_simustudy.R: wrapper R function to call .stan file for inference in simulated datasets (just a simplified version of utils_forstan_all_priormiss.R) - utils_plotsfinalsimustudy_para.R: functions to generate plots of the simulation study results - utils_simulatedata.R: functions to simulate data (useful for simulation study, assessing model fit, computing SAR, etc.) - FinalFigures: contains code to generate paper’s main figures, as well as SAR, model fit on seroprevalence, and second simulation study. - FinalSimuStudy_gammaln15: contains code for the simulation study: - Launch_Rscript.sh: bash file that calls mainLaunch.R for the parameter combinations specified in Launch.R - mainLaunch.R: can be ran alone specifying a set of parameter values - testtry: contains an example of a run of mainLaunch.R - formatted_data: contains the full data (without filtering on hhsize, maxNA or age missingness) for 3 studies (Yaoundé, Conakry and Kinshasa). The Lubumbashi dataset is not provided.Also covid data for the 3 countries of the study (to compute overall SAR) (to create figs 1 and 2) - MCMC_results: contains the results of the inference for the real datasets: - allwithKinshasaAntiS: cont …