euromomo/FluMOMO_v42.R

   1 # Install required packages (if not already installed)
   2 #install.packages("ISOweek")
   3
   4
   5 ### Clear enviromnet i.e. delete all data and variabels
   6 rm(list = ls())
   7 # Clear console
   8 cat("\014")
   9
  10 ### Country
  11 country <- ""
  12 country.code <- ""
  13
  14 ### Work directory - directory where the R programs are placed
  15 wdir <- "."
  16
  17 ### Period: Start and end (both included)
  18 start_year <- 2013
  19 start_week <- 40
  20 end_year <- 2018
  21 end_week <- 40
  22
  23 ### Deaths data source
  24 ### Must be placed in the subdirectory /data in the work directory
  25 # 1 = A-MOMO complete file, renamed to A-MOMO data.txt
  26 # 0 = you provide a ;-separated file: deaths.txt, containing at least the variable: agegrp, year, week, deaths
  27 A_MOMO <- 1
  28
  29 ### Weather data source
  30 # 1 = automatic download from EuroMOMO website
  31 # 0 = you provide a ;-separated file: wdata_'country.code'.txt, containing at least the variables: date, pop3, NUTS3, temp and placed in the subdirectory /data in the work directory
  32 WeatherData <- 1
  33
  34 ### Population data (TRUE/FALSE)
  35 ### A ;-separated file: population.txt, must be placed in the subdirectory /data in the work directory
  36 population <- FALSE
  37
  38 # Restrict IA to only positive (TRUE/FALSE)
  39 IArest <- TRUE
  40
  41 # Number of IA lags
  42 # 0 = no lag, 1 = one week lag, ...(max=9)
  43 IAlags <- 2
  44
  45 # Number of OF lags
  46 # 0 = no lag, 1 = one week lag, ...(max=9)
  47 ETlags <- 2
  48
  49
  50 ### Directory setup ######################################################################
  51
  52 ### Create general output dir
  53 if (!dir.exists(paste0(wdir,"/FluMOMO_",end_year,"w",formatC(end_week, width=2, flag="0")))) {
  54   dir.create(paste0(wdir,"/FluMOMO_",end_year,"w",formatC(end_week, width=2, flag="0")))
  55 }
  56 ### Copy data directory - directory where input data are stored
  57 indir <- paste0(wdir,"/FluMOMO_",end_year,"w",formatC(end_week, width=2, flag="0"),"/data")
  58 if (!dir.exists(indir)) dir.create(indir)
  59 file.copy(from = list.files(paste0(wdir,"/data"), all.files = TRUE, full.names = TRUE, no.. = TRUE),
  60           to = indir, overwrite = TRUE, recursive = FALSE, copy.mode = TRUE)
  61 #file.remove(list.files(paste0(wdir,"/data"), all.files = TRUE, full.names = TRUE, no.. = TRUE))
  62
  63 ### Create output directory - directory where output are created
  64 outdir <- paste0(wdir,"/FluMOMO_",end_year,"w",formatC(end_week, width=2, flag="0"),"/output")
  65 if (!dir.exists(outdir)) dir.create(outdir)
  66 #########################################################################################
  67
  68 # Estimation
  69 source(paste0(wdir,"/Estimation_v42.R"), echo = FALSE)
  70 # Output: txt-files
  71 source(paste0(wdir,"/Output_txt_v42.R"))
  72 # Output: graphs IA and ET
  73 source(paste0(wdir,"/Output_IA_ET_v42.R"))
  74 # Output: graphs over calendar time
  75 source(paste0(wdir,"/Output_calendar_v42.R"))
  76 # Output: graphs cumulated IA
  77 source(paste0(wdir,"/Output_cumulated_v42.R"))