suicide_cost_step1.R

if(Sys.info()[4] %in% c("LAZ-ID1",
                        "LAZ-ID2",
                        "LAZ-DEID1",
                        "LAZ-DEID2")){
  setwd("E:/CT_APCD/Sai/suicide_cost")
}
library(methods)
source("utils.R")
need_pkgs <- c("data.table", "bit64", "tools", "touch", 
               "dplyr", "lubridate", "tidyverse", "matrixStats")
need.packages(need_pkgs)
source("get_suicide_attempts.R")

# dgxcols <- c("MEDICAL_CLAIM_SERVICE_LINE_ID",
#              "ICD_VERSION_IND", "DIAGNOSIS_CODE")
cols <- c("first_service_dt", "INTERNAL_MEMBER_ID",
          "ICD_VERSION_IND", "DIAGNOSIS_CODE",
          "MEDICAL_CLAIM_SERVICE_LINE_ID")
# elig_pt <- fread(paste0("E:/CT_APCD/shared/intermediate_data/", 
#                         "APCD_modified/eligibility/By_Fiscal_Year/", 
#                         "medical_elig_all.csv"),
#                  colClasses = "character",
#                  select = c("INTERNAL_MEMBER_ID",
#                             "birth_dt",
#                             "FiscalYR")) %>% unique(use.key = FALSE)
for (yr in 2013:2017){
  cat(paste0("begin ", yr, " at ", Sys.time(), "\n"))
  # mcpt <- fread(paste0("E:/CT_APCD/shared/intermediate_data/", 
  #                      "APCD_modified/medicare_medicare_ad_patients/", 
  #                      "fy", yr, "all_ages.csv"),
  #               colClasses = "character")
  # elig_pt1 <- elig_pt[FiscalYR == yr]
  mc <- fread(paste0("E:/CT_APCD/Sai/intermediate_data/", 
                     "cost_measure_intermediate_data/", 
                     "medical_fiscalyear_", yr, ".csv"), 
              colClasses = "character",
              select = cols)
  dgx <- fread(paste0("output/dgx_", yr, ".csv"),
               colClasses = "character")
  mc_dgx <- rbind(dgx, mc) %>% unique(use.key = FALSE)
  fwrite(mc_dgx, file = paste0("output/mc_dgx_unique_",
                               yr, ".csv"))
  rm(mc, dgx, mc_dgx)
  gc()
  cat(paste0(yr, " done at ", Sys.time(), "\n"))
}