euromomo/Output_txt_v42.R

   1 ### ;-separated txt files ###
   2
   3 if (IArest) {
   4   results4 <- read.table(file=paste0(outdir,"/",country,"_output_v4_IArestricted.txt"),
   5       header = TRUE, sep =";", dec=".")
   6 } else {
   7   results4 <- read.table(file=paste0(outdir,"/",country,"_output_v4.txt"),
   8       header = TRUE, sep =";", dec=".")
   9 }
  10
  11 csvout <- function(x, s) {
  12   y <- do.call("rbind", lapply(sort(unique(x[,s])), function(i) {
  13     cbind(unique(x[,"agegrp"]), min(x[(x[,s]==i),"yw"]), max(x[(x[,s]==i),"yw"]),
  14         round(tail(
  15           x[(x[,s]==i),
  16               c(paste0("cEdIA_",s), paste0("cEdIA_",s,"_95L"), paste0("cEdIA_",s,"_95U"),
  17               paste0("cEdET_",s), paste0("cEdET_",s,"_95L"), paste0("cEdET_",s,"_95U"),
  18               paste0("cexcess_",s), paste0("cuexcess_",s), "N")],
  19           n=1)))
  20     }))
  21   colnames(y) <- c("AgeGroup", "Start", "End", "cIA", "cIA_95L", "cIA_95U",
  22                     "cET", "cET_95L", "cET_95U", "cexcess", "cuexcess", "N")
  23   return(y)
  24 }
  25
  26 results4$yw <- sprintf("%04iw%02i",results4$year, results4$week)
  27
  28 for (s in c("summer","winter","year")) {
  29   out <- do.call("rbind", lapply(0:4, function(a) {
  30     csvout(results4[(!is.na(results4[,s])) & (results4$agegrp==a),], s)
  31   }))
  32   out$AgeGroup <- factor(out$AgeGroup, levels = c(0,1,2,3,4),
  33         labels = c("0-4 years","5-14 years","15-64 years","Aged 65","Total"))
  34   write.table(out[,c("AgeGroup", "Start", "End", "cIA", "cIA_95L", "cIA_95U",
  35               "cET", "cET_95L", "cET_95U", "cexcess", "cuexcess")],
  36       file = paste0(outdir, "/", s, "_deaths_v4_IA", ifelse(IArest, "restricted", ""), ".txt" ),
  37       row.names = FALSE, quote = FALSE, sep =";", dec=".", na="")
  38   if (population) {
  39     out[,c("cIA", "cIA_95L", "cIA_95U", "cET", "cET_95L", "cET_95U", "cexcess", "cuexcess")] <-
  40       round(100000 * out[,c("cIA", "cIA_95L", "cIA_95U", "cET", "cET_95L", "cET_95U", "cexcess", "cuexcess")] / out[,"N"], 2)
  41     colnames(out) <- c("AgeGroup", "Start", "End", "cmrIA", "cmrIA_95L", "cmrIA_95U", "cmrET", "cmrET_95L", "cmrET_95U", "cexcess", "cuexcess", "N")
  42     write.table(out[,c("AgeGroup", "Start", "End", "cmrIA", "cmrIA_95L", "cmrIA_95U",
  43               "cmrET", "cmrET_95L", "cmrET_95U", "cexcess", "cuexcess")],
  44       file=paste0(outdir,"/",s,"_mr_v4_IA", ifelse(IArest, "restricted", ""), ".txt"),
  45       row.names = FALSE, quote = FALSE, sep =";", dec=".")
  46   }
  47 }
  48
  49 rm(out, s, csvout, results4)