Removed data files

[covid19.git] / euromomo / FluMOMO_v42.R

diff --git a/euromomo/FluMOMO_v42.R b/euromomo/FluMOMO_v42.R
deleted file mode 100644 (file)
index 3372f23..0000000
--- a/euromomo/FluMOMO_v42.R
+++ /dev/null
@@ -1,77 +0,0 @@
-# Install required packages (if not already installed)\r
-#install.packages("ISOweek")\r
-\r
-\r
-### Clear enviromnet i.e. delete all data and variabels\r
-rm(list = ls())\r
-# Clear console\r
-cat("\014")\r
-\r
-### Country\r
-country <- ""\r
-country.code <- ""\r
-\r
-### Work directory - directory where the R programs are placed\r
-wdir <- "."\r
-\r
-### Period: Start and end (both included)\r
-start_year <- 2013\r
-start_week <- 40\r
-end_year <- 2018\r
-end_week <- 40\r
-\r
-### Deaths data source\r
-### Must be placed in the subdirectory /data in the work directory\r
-# 1 = A-MOMO complete file, renamed to A-MOMO data.txt\r
-# 0 = you provide a ;-separated file: deaths.txt, containing at least the variable: agegrp, year, week, deaths\r
-A_MOMO <- 1\r
-\r
-### Weather data source\r
-# 1 = automatic download from EuroMOMO website\r
-# 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\r
-WeatherData <- 1\r
-\r
-### Population data (TRUE/FALSE)\r
-### A ;-separated file: population.txt, must be placed in the subdirectory /data in the work directory\r
-population <- FALSE\r
-\r
-# Restrict IA to only positive (TRUE/FALSE)\r
-IArest <- TRUE\r
-\r
-# Number of IA lags\r
-# 0 = no lag, 1 = one week lag, ...(max=9)\r
-IAlags <- 2\r
-\r
-# Number of OF lags\r
-# 0 = no lag, 1 = one week lag, ...(max=9)\r
-ETlags <- 2\r
-\r
-\r
-### Directory setup ######################################################################\r
-\r
-### Create general output dir\r
-if (!dir.exists(paste0(wdir,"/FluMOMO_",end_year,"w",formatC(end_week, width=2, flag="0")))) {\r
-  dir.create(paste0(wdir,"/FluMOMO_",end_year,"w",formatC(end_week, width=2, flag="0")))\r
-}\r
-### Copy data directory - directory where input data are stored\r
-indir <- paste0(wdir,"/FluMOMO_",end_year,"w",formatC(end_week, width=2, flag="0"),"/data")\r
-if (!dir.exists(indir)) dir.create(indir)\r
-file.copy(from = list.files(paste0(wdir,"/data"), all.files = TRUE, full.names = TRUE, no.. = TRUE),\r
-          to = indir, overwrite = TRUE, recursive = FALSE, copy.mode = TRUE)\r
-#file.remove(list.files(paste0(wdir,"/data"), all.files = TRUE, full.names = TRUE, no.. = TRUE))\r
-\r
-### Create output directory - directory where output are created\r
-outdir <- paste0(wdir,"/FluMOMO_",end_year,"w",formatC(end_week, width=2, flag="0"),"/output")\r
-if (!dir.exists(outdir)) dir.create(outdir)\r
-#########################################################################################\r
-\r
-# Estimation\r
-source(paste0(wdir,"/Estimation_v42.R"), echo = FALSE)\r
-# Output: txt-files\r
-source(paste0(wdir,"/Output_txt_v42.R"))\r
-# Output: graphs IA and ET\r
-source(paste0(wdir,"/Output_IA_ET_v42.R"))\r
-# Output: graphs over calendar time\r
-source(paste0(wdir,"/Output_calendar_v42.R"))\r
-# Output: graphs cumulated IA\r
-source(paste0(wdir,"/Output_cumulated_v42.R"))\r