09.tables.R

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# Updated version of the R code for the analysis in:
#
#  "Scortichini M, Schneider Dos Santos R, De' Donato F, De Sario M,
#    Michelozzi P, Davoli M, Masselot P, Sera F, Gasparrini A.
#    Excess mortality during the COVID-19 outbreak in Italy: a two-stage
#    interrupted time-series analysis.
#    International Journal of Epidemiology. 2020. DOI: 10.1093/ije/dyaa169."
#  http://www.ag-myresearch.com/2020_scortichini_ije.html
#
# Update: 21 October 2020
# * an updated version of this code, compatible with future versions of the
#   software, is available at:
#   https://github.com/gasparrini/ItalyCOVIDdeath
################################################################################

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# TABLES
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# TABLE 1: DESCRIPTIVE BY REGION

# CREATE THE MAIN TABLE
datatab1 <- datafull %>%
  group_by(regcode, regname) %>%
  summarize(prov=length(unique(provcode)), 
    munic=length(unique(municcode)), 
    cov=length(unique(municcode[munictype==1]))/munic*100,
    tot=sum(tot, na.rm=T)) %>%
  ungroup() %>%
  dplyr::select(-regcode)

# ADD AREA
datatab1 <- cbind(datatab1[,1], Area=areareg, datatab1[,-1])

# ADD THE TOTAL FOR COUNTRY
datatab1[nrow(datatab1)+1,] <- data.frame(regname="Italy", "",
  prov=sum(datatab1$prov), munic=sum(datatab1$munic), 
  cov=sum(datatab1$munic*datatab1$cov)/sum(datatab1$munic),
  tot=sum(datatab1$tot))

# FORMAT AND NAMES
for(i in c(3,4,6)) datatab1[,i] <- formatC(datatab1[,i,drop=T], format="f",
  digits=0, big.mark=",")
datatab1[-nrow(datatab1),1] <- labreg
datatab1[,5] <- paste0(formatC(datatab1[,5,drop=T], format="f", digits=1), "%")
names(datatab1) <- c("Region", "Area", "Provinces", "Municipalities", "Coverage",
  "Deaths")

# SAVE
write.csv(datatab1, file="tables/tab1.csv", row.names=F)

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# TABLE 2: EXCESS BY REGION

tab2list <- lapply(sexlab, function(x) {
  
  # COMPUTE EXCESS AND TOTAL
  exc <- excreg[,1,x,1,]
  tot <- totreg[,1,x,1]
  
  # ADD TOTAL FOR COUNTRY
  exc <- rbind(exc, round(excitaly[1,x,1,]))
  tot <- c(tot, totitaly[1,x,1])
  rownames(exc)[nrow(exc)] <- "Italy"

  # FORMAT
  tot <- formatC(tot, format="f", digits=0, big.mark=",")
  exc <- formatC(exc, format="f", digits=0, big.mark=",", zero.print="0")

  # TABLE
  tab <- cbind(tot, paste0(exc[,1]," (",exc[,2]," to ", exc[,3],")"))
  dimnames(tab) <- list(rownames(exc), paste(c("Death", "Excess"),x))
  tab
})

datatab2 <- do.call(cbind, tab2list)

# SAVE
write.csv(datatab2, file="tables/tab2.csv", row.names=T)