# Script to reproduce Supplementary Table 1 from:
#
# Tim K. Tsang, Vicky J. Fang, Dennis K. M. Ip, Ranawaka A. P. M. Perera, Hau Chi So, Gabriel M. Leung, J. S. Malik Peiris, Benjamin J. Cowling and Simon Cauchemez

# Indirect protection from vaccinating children against influenza in households.
# Nature Communications 2019.

library(chron)

b <- read.csv("data_long.csv")

names(b)[5:7*2] <- c("AT0","AT1","AT2")

b$date0 <- as.numeric(as.character(b$date0))
b$date1 <- as.numeric(as.character(b$date1))
b$date2 <- as.numeric(as.character(b$date2))

###################################################################################################
table_function <- function(data){

a <- matrix(NA,10,2)

a[1,1] <- nrow(data)
a[3,1] <- sum(data$age <= 18 & !is.na(data$age))
a[4,1] <- sum(data$age > 18 & !is.na(data$age))
a[5,1] <- sum(data$male == 1 & !is.na(data$male))
a[6,1] <- sum(data$vac == 1 & !is.na(data$vac))
a[8,1] <- sum(!is.na(data$AT0))
a[9,1] <- sum(!is.na(data$AT1))
a[10,1] <- sum(!is.na(data$AT2))

a[c(3:6,8:10),2] <- round(a[c(3:6,8:10),1]/nrow(data)*100,1)

c <- paste(a[,1]," (",a[,2],"%)",sep="")

c[1] <- a[1,1]


return(c)
}

###################################################################################################

table <- matrix(NA,10,2)

table[,1] <- table_function(b[b$group==0&b$member!=0,])
table[,2] <- table_function(b[b$group==1&b$member!=0,])

table[grepl("NA",table)] <- " "

write.csv(table,"TableS1.csv")