DOI: 10.5061/dryad.cj62621
title: Data from: Indirect protection from vaccinating children against influenza in households

description: Vaccination is an important intervention to prevent influenza virus
 infection, but indirect protection of household members of vaccinees is
 not fully known. Here, we analyze a cluster household randomized control
 trial, with one child in each household randomized to receive vaccine or
 placebo, for an influenza B epidemic in Hong Kong. We apply statistical
 models to estimate household transmission dynamics and quantify the direct
 and indirect protection of vaccination. Direct vaccine efficacy is 71%.
 The infection probability of unvaccinated household members in vaccinated
 households was only 5% lower than in control households, because only 10%
 of infections are attributed to household transmission. Even when that
 proportion rises to 30% and all children are vaccinated, we predict that
 the infection probability for unvaccinated household members is only
 reduced by 20%. This suggests that benefits of individual vaccination
 remain important even when other household members are vaccinated.
description: Read me (data file
 explanations)Data
 fileThis data file contains
 data from the kiddivax study at 2009-2010. This is in a wide format that
 each row is a household.data.csvData fileThis is the long format that each row is a participant.data_long.csvData fileThis is the format that each row is a participant for each round.data_round.csvInfluenza surveillance dataThe influenza proxy used in the analysis.ILILAB.csvData fileThis file contains information on the baseline titer distribution.sub_inf.csvData file (MCMC result)The mcmc result for the manuscript.mcmc_result.csvR syntax to fit the digraph modelR syntax to fit the digraph model on the household data. This will create a data file [mcmc_result.csv] for further analysis. Noted that Supplementary Table 5 was also generated from this file.indirect_benefit_main.RR syntaxThe file that are used by [indirect_benefit_main.r].indirect_benefit.cppR syntaxThe file that are used by [prediction.R].indirect_benefit_prediction.cppR syntax to condcut predictionR syntax to condcut prediction based on the posterior distribution of model parameter [mcmc_result.csv].prediction.RR syntax to generate prediciton for different scenariosR syntax to use [prediction.R] file to generate prediciton for different scenarios. This should generate 15 files in the format of [predictionVW.Rdata]: V: 1: no vaccination in households. 2: vaccinating one child in households. 3: vaccination all children in households W: 1-5 for the proportion of infection attributed to household transmission is 10% (1), 20% (2), 30% (3), 40% (4) and 50% (5).prediction_generator.RR syntax for Figure 2Contain the R syntax to reproduce Figure 2.Figure_2.RR syntax for Figure 3Contain the R syntax to reproduce Figure 3.Figure_3.RR syntax for Figure 4Contain the R syntax to reproduce Figure 4.Figure_4.RR syntax for Figure 5 & S_Figure 1-5Contain the R syntax to reproduce Figure 5 in the main text, and supplementary Figure 1-5.Figure_5.RR syntax for Supplementary Table 1R syntax to reproduce results in Supplementary Table 1.Table_S1.RR syntax for Supplementary Table 2-4R syntax to reproduce results in Supplementary Table 2,3 and 4.Table_S2_3_4.RR syntax for Supplementary Table 6R syntax to reproduce results in Supplementary Table 6.Table_S6.R