The data and R code in these files produce the results in the manuscript "Model-based estimates of age-structured SARS-CoV-2 epidemiology in households."
"householdData2021.txt" contains the household data used by the analyses in the manuscript. Each row represents an individual participant. The “houseID” column is the ID of the household where the individual reportedly lived. Only households with full participation were included, so the number of rows sharing the same houseID is equal to the reported total household size. The “ageCategory” column indicates the age group of the participant, with letters a through h indicating the age ranges defined in the manuscript (Table 1). The “numVaccineDoses” column gives the survey-reported number of doses of COVID-19 vaccine that the participant had received prior to data collection. The “vaccineDose1interval” and “vaccineDose2interval” columns give the number of days between the survey-reported date of each vaccine dose and the date of participant blood sample collection; NA means that the vaccine dose was not received, or a valid date was not reported. The “priorTest” column contains P if the participant reported on the survey that they had received a positive COVID-19 test result in the past and contains N if they did not. The “AbottResult” and “EuroimmunResult” and “SiemensResult” columns contain data from each of the three antibody tests described in the manuscript: P for positive, N for negative, and X means either the test was not performed or produced a result that was not positive or negative.
"getMLE.R" contains R code that produces the maximum likelihood estimates found in the Results section and Supplementary Information of the manuscript. The code runs one set of model estimates at a time, and the model specification can be changed where indicated in the code using one of the model names listed in the file “resultTableSettings.txt.” The code also makes use of the commands and functions defined in the files “specifyModel.R,” “dataPreparationFunctions.R,” “transmissionPrepFunctions.R,” and “MLEfunctions.R.”
“Figure1transmissionMechanisms.R” and “Figure2infectionRiskByAge.R” contain R code that produced Figures 1 and 2 in the manuscript.