Data from: Indirect protection from vaccinating children against influenza in households

Tsang TK, Fang VJ, Ip DKM, Perera RAPM, So HC, Leung GM, Peiris JSM, Cowling BJ, Cauchemez S

Date Published: January 10, 2019

DOI: https://doi.org/10.5061/dryad.cj62621

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Title Read me (data file explanations)
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Title Data file
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Description This data file contains data from the kiddivax study at 2009-2010. This is in a wide format that each row is a household.
Download data.csv (81.67 Kb)
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Title Data file
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Description This is the long format that each row is a participant.
Download data_long.csv (123.7 Kb)
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Title Data file
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Description This is the format that each row is a participant for each round.
Download data_round.csv (175.5 Kb)
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Title Influenza surveillance data
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Description The influenza proxy used in the analysis.
Download ILILAB.csv (24.4 Kb)
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Title Data file
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Description This file contains information on the baseline titer distribution.
Download sub_inf.csv (42 bytes)
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Title Data file (MCMC result)
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Description The mcmc result for the manuscript.
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Title R syntax to fit the digraph model
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Description R 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.
Download indirect_benefit_main.R (4.935 Kb)
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Title R syntax
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Description The file that are used by [indirect_benefit_main.r].
Download indirect_benefit.cpp (53.33 Kb)
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Title R syntax
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Description The file that are used by [prediction.R].
Download indirect_benefit_prediction.cpp (61.72 Kb)
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Title R syntax to condcut prediction
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Description R syntax to condcut prediction based on the posterior distribution of model parameter [mcmc_result.csv].
Download prediction.R (5.267 Kb)
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Title R syntax to generate prediciton for different scenarios
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Description R 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).
Download prediction_generator.R (1.19 Kb)
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Title R syntax for Figure 2
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Description Contain the R syntax to reproduce Figure 2.
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Title R syntax for Figure 3
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Description Contain the R syntax to reproduce Figure 3.
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Title R syntax for Figure 4
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Description Contain the R syntax to reproduce Figure 4.
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Title R syntax for Figure 5 & S_Figure 1-5
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Description Contain the R syntax to reproduce Figure 5 in the main text, and supplementary Figure 1-5.
Download Figure_5.R (14.35 Kb)
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Title R syntax for Supplementary Table 1
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Description R syntax to reproduce results in Supplementary Table 1.
Download Table_S1.R (1.462 Kb)
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Title R syntax for Supplementary Table 2-4
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Description R syntax to reproduce results in Supplementary Table 2,3 and 4.
Download Table_S2_3_4.R (10.65 Kb)
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Title R syntax for Supplementary Table 6
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Description R syntax to reproduce results in Supplementary Table 6.
Download Table_S6.R (1.649 Kb)
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When using this data, please cite the original publication:

Tsang TK, Fang VJ, Ip DKM, Perera RAPM, So HC, Leung GM, Peiris JSM, Cowling BJ, Cauchemez S (2019) Indirect protection from vaccinating children against influenza in households. Nature Communications 10(1): 106. https://doi.org/10.1038/s41467-018-08036-6

Additionally, please cite the Dryad data package:

Tsang TK, Fang VJ, Ip DKM, Perera RAPM, So HC, Leung GM, Peiris JSM, Cowling BJ, Cauchemez S (2019) Data from: Indirect protection from vaccinating children against influenza in households. Dryad Digital Repository. https://doi.org/10.5061/dryad.cj62621
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