run_pmed.R

# Create directory ------------------------------------------------------------

tbl_dir <- "data_tables/hc_pmed"
dir.create(tbl_dir)

# Define groups ---------------------------------------------------------------
row_grps <- pmed_grps 
col_grps <- "ind"

# Run for specified year(s) ---------------------------------------------------
for(year in year_list) {
  dir.create(sprintf('%s/%s', tbl_dir, year))

  yr <- substring(year, 3, 4)

# Load files and define svydesigns --------------------------------------------
  source("code/load_fyc.R",  echo = T) # Load FYC file
  source("code/load_pmed.R", echo = T) # Load RX event files
  source("code/dsgn_pmed.R", echo = T) # Define all survey design objects

# Run for prescribed medicines ------------------------------------------------
  res <- list()
  res[["totPOP"]] <- svyby(~count, by = ~RXDRGNAM, FUN = svytotal, design = DRGdsgn)
  res[["totEXP"]] <- svyby(~RXXPX, by = ~RXDRGNAM, FUN = svytotal, design = DRGdsgn)
  res[["totEVT"]] <- svyby(~n_RX,  by = ~RXDRGNAM, FUN = svytotal, design = DRGdsgn)
  res[["n"]]      <- svyby(~count, by = ~RXDRGNAM, FUN = unwtd.count, design = DRGdsgn)

  # Format and output to csv
  for(stat in names(res)) {
    res[[stat]] %>%
      setNames(c("rowLevels", stat, p(stat, "_se"))) %>%
      mutate(rowGrp = "RXDRGNAM", colGrp = "ind", colLevels = "Total") %>%
      update.csv(file = sprintf("%s/%s.csv", year, stat), dir = tbl_dir)
  }

# Run for therapeutic classes -------------------------------------------------
  res <- list()
  res[["totPOP"]] <- svyby(~count, by = ~TC1name, FUN = svytotal, design = TC1dsgn)
  res[["totEXP"]] <- svyby(~RXXPX, by = ~TC1name, FUN = svytotal, design = TC1dsgn)
  res[["totEVT"]] <- svyby(~n_RX,  by = ~TC1name, FUN = svytotal, design = TC1dsgn)
  res[["n"]]      <- svyby(~count, by = ~TC1name, FUN = unwtd.count, design = TC1dsgn)

  # Format and output to csv
  for(stat in names(res)) {
    res[[stat]] %>%
      setNames(c("rowLevels", stat, p(stat, "_se"))) %>%
      mutate(rowGrp = "TC1name", colGrp = "ind", colLevels = "Total") %>%
      update.csv(file = sprintf("%s/%s.csv", year, stat), dir = tbl_dir)
  }

} # END for year in year_list