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comorbitiies.R
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comorbitiies.R
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# Create indicator variables for the following mental illness types in the medical data
if(Sys.info()[4] %in% c("LAZ-ID1",
"LAZ-ID2",
"LAZ-DEID1",
"LAZ-DEID2")){
setwd("E:/CT_APCD/Sai/suicide_cost")
}
rm(list=ls())
library(methods)
source("utils.R")
need_pkgs <- c("data.table", "bit64", "tools", "touch",
"dplyr", "lubridate", "tidyverse", "matrixStats",
"knitr", "plyr", "haven")
need.packages(need_pkgs)
source("E:/CT_APCD/Sai/2019spring/sim_healthcare_cost_measures/R/functions.R")
cmb_code1 <- c(339, 346, "307.81", "784.0", "350.2")
cmb_code2 <- c("337.0", "337.1", 355:357, 377)
cmb_code3 <- c("338.21", "338.22", "338.28", "338.29", "338.4",
346, "307.81", "71x", "72x")
cmb_code4 <- c("282.62", "338.11", "338.12", "338.18","338.19",
"522.5", "522.7", 574, 577, 592, "733.1",
"80x", "81x", "82x", "83x", "86x", "87x",
840:848, 850:854, 880:887, 890:897, 900:904, 91:95)
cmb_code5 <- c(140:172, 174:239, 3383)
cmb_code6 <- c("293.83", "296.2", "296.3", "296.90", (29691:29699)/100, "298.0", "300.4",
"301.12", "309.0", "309.1", 311, "296.0", "296.1", (2964:2968)/10)
cmb_code6 <- c("295.0", (2951:2954)/10, (2956:2959)/10, "297.0",
(2971:2973)/10, "297.8", "297.9", "298.0", (2981:2984)/10,
"298.8", "298.9")
cmb_code7 <- c("291", "292", "303.0", "303.9", (3041:3049)/10,
"305.0", (3052:3054)/10, (3056:3059)/10)
cmb_code8 <- c("309.81")
cmb_code9 <- c("300.00", "300.01", "300.02",
"300.09", "300.10", "300.20", (30021:30023)/100, "300.29")
cmb_code <- c(cmb_code1, cmb_code2, cmb_code3, cmb_code4, cmb_code5, cmb_code6, cmb_code7,
cmb_code8, cmb_code9)
(cmb_code_9 <- touch::icd_map(cmb_code, 9, 10, method = "reverse"))
col_mc <- c("MEDICAL_CLAIM_SERVICE_LINE_ID",
"SUBMITTER_ID",
"PRODUCT_CODE",
"INTERNAL_MEMBER_ID",
"first_service_dt",
"last_service_dt",
"ADMISSION_DT",
"discharge_dt",
"PLACE_OF_SERVICE_CODE",
"TYPE_OF_BILL_CODE",
"CLAIM_TYPE_ID",
"TYPE_OF_SETTING_ID",
"PLACE_OF_SETTING_ID",
"QUANTITY",
"CHARGE_AMT",
"PAID_AMT",
"CLAIM_STATUS_CODE",
"PROCEDURE_CODE",
"REVENUE_CODE",
"ICD_VERSION_IND",
"DIAGNOSIS_CODE",
"ICD_PROCEDURE_CODE",
"ORPHANED_ADJUSTMENT_FLAG",
"DENIED_CLAIM_FLAG",
"EMERGENCY_ROOM_FLAG",
"MEDICAL_CLAIM_HEADER_ID",
"RENDERING_PROVIDER_ID",
"BILLING_PROVIDER_ID",
"ATTENDING_PROVIDER_ID",
"REFERRING_PROVIDER_ID")
scpt <- unique(fread('output/sc_15_no_sc_13_14.csv', colClasses = 'character',
select = c("INTERNAL_MEMBER_ID")))[, sc_flag := 1]
noscpt <- fread('output/no_sc_2013_2015_pt.csv', colClasses = 'character')[, sc_flag := 0]
pt <- rbind(scpt, noscpt)
## medical claim
for(yr in 2014:2017){
cat(paste0("begin ", yr, " at ", Sys.time(), "\n"))
mc_dgx <- fread(paste0("output/", "mc_dgx_unique_",
yr, ".csv"),
colClasses = "character")[INTERNAL_MEMBER_ID %in% pt$INTERNAL_MEMBER_ID]
mc[, `:=`(cmb_flag = 0)]
names(mc)
mc[INTERNAL_MEMBER_ID %in% scpt$INTERNAL_MEMBER_ID, sc_pt_flag := 1]
pc <- rbindlist(lapply(yr:(yr - 1), function(x){
# rt <- data.table(read_sas(paste0("E:/CT_APCD/Beth/data4/Commercial/new_intermediate_files/med",
# sub('.*(?=.{2}$)', '',
# x, perl = T),
# "_com_primary_care.sas7bdat")))
rt <- fread(paste0("E:/CT_APCD/Sai/intermediate_data/",
"cost_measure_intermediate_data/value_sets/pc_",
yr, ".csv"),
colClasses = "character",
select = c("INTERNAL_MEMBER_ID", "MEDICAL_CLAIM_SERVICE_LINE_ID",
"first_service_dt"))[INTERNAL_MEMBER_ID %in% pt$INTERNAL_MEMBER_ID]
return(rt)
}))
pc <- pc[ymd(first_service_dt) >= ymd(paste0(yr - 1, '-10-01')) &
ymd(first_service_dt) <= ymd(paste0(yr, '-09-30'))]
ip <- get_medical_vs(vs.list = c("Acute Inpatient",
"Inpatient Stay",
"Nonacute Inpatient",
"Nonacute Inpatient Stay"),
year.list = (yr - 1):yr,
code.sys = c("revenue_code", "procedure_code"),
select = NULL,
dir.raw = paste0("E:/CT_APCD/shared/intermediate_data/",
"APCD_modified/value_set/",
"medical_claim/"),
takeUnique = TRUE,
fill = TRUE,
tolower = FALSE)
ip <- ip[, c("internal_member_id",
"medical_claim_service_line_id",
"first_service_dt")]
setnames(ip,
c("internal_member_id",
"medical_claim_service_line_id"),
c("INTERNAL_MEMBER_ID",
"MEDICAL_CLAIM_SERVICE_LINE_ID"))
ip <- ip[INTERNAL_MEMBER_ID %in% pt$INTERNAL_MEMBER_ID]
ip[, first_service_dt := ymd(mdy(first_service_dt))]
ip <- ip[ymd(first_service_dt) >= ymd(paste0(yr - 1, '-10-01')) &
ymd(first_service_dt) <= ymd(paste0(yr, '-09-30'))]
sum(!ip$MEDICAL_CLAIM_SERVICE_LINE_ID %in% mc$MEDICAL_CLAIM_SERVICE_LINE_ID)
op <- get_medical_vs(vs.list = c("Outpatient"),
year.list = (yr - 1):yr,
code.sys = c("revenue_code", "procedure_code"),
select = NULL,
dir.raw = paste0("E:/CT_APCD/shared/intermediate_data/",
"APCD_modified/value_set/",
"medical_claim/"),
takeUnique = TRUE,
fill = TRUE,
tolower = FALSE)
op <- op[, c("internal_member_id",
"medical_claim_service_line_id",
"first_service_dt")]
setnames(op,
c("internal_member_id",
"medical_claim_service_line_id"),
c("INTERNAL_MEMBER_ID",
"MEDICAL_CLAIM_SERVICE_LINE_ID"))
op <- op[INTERNAL_MEMBER_ID %in% pt$INTERNAL_MEMBER_ID]
op[, first_service_dt := ymd(mdy(first_service_dt))]
op <- op[ymd(first_service_dt) >= ymd(paste0(yr - 1, '-10-01')) &
ymd(first_service_dt) <= ymd(paste0(yr, '-09-30'))]
sum(!op$MEDICAL_CLAIM_SERVICE_LINE_ID %in% mc$MEDICAL_CLAIM_SERVICE_LINE_ID)
names(mc)
mc[INTERNAL_MEMBER_ID %in% pc$MEDICAL_CLAIM_SERVICE_LINE_ID,
pc_flag := 1]
mc[INTERNAL_MEMBER_ID %in% ip$MEDICAL_CLAIM_SERVICE_LINE_ID,
ip_flag := 1]
mc[INTERNAL_MEMBER_ID %in% op$MEDICAL_CLAIM_SERVICE_LINE_ID,
op_flag := 1]
fwrite(mc,
file = paste0("output/files_2021_summer/mc_sc_vs_nosc_", yr, ".csv"))
rm(mc, pc, ip, op)
gc()
cat(paste0(yr, " done at ", Sys.time(), "\n"))
}
## dgx
for(yr in 2013:2016){
cat(paste0("begin ", yr, " at ", Sys.time(), "\n"))
mc <- fread(paste0("output/files_2021_summer/mc_sc_vs_nosc_", yr, ".csv"),
colClasses = "character",
select = c("MEDICAL_CLAIM_SERVICE_LINE_ID",
"sc_pt_flag",
"pc_flag",
"ip_flag",
"op_flag" ))
dgx <- fread(paste0("output/dgx_", yr, ".csv"),
colClasses = "character")
dgx <- dgx[mc, on = "MEDICAL_CLAIM_SERVICE_LINE_ID", nomatch = 0]
fwrite(dgx,
file = paste0("output/files_2021_summer/dgx_sc_vs_nosc_", yr, ".csv"))
rm(mc, dgx)
gc()
cat(paste0(yr, " done at ", Sys.time(), "\n"))
}
## icd procedure
icd_p <- fread("E:/CT_APCD/Uconn_extract_20180521_12312017/MEDICAL_CLAIM_ICD_PROCEDURE.txt",
colClasses = "character")
for(yr in 2013:2017){
cat(paste0("begin ", yr, " at ", Sys.time(), "\n"))
mc <- fread(paste0("output/files_2021_summer/mc_sc_vs_nosc_", yr, ".csv"),
colClasses = "character",
select = c("MEDICAL_CLAIM_SERVICE_LINE_ID",
"sc_pt_flag",
"pc_flag",
"ip_flag",
"op_flag" ))
icd_p2 <- icd_p[mc, on = "MEDICAL_CLAIM_SERVICE_LINE_ID", nomatch = 0]
fwrite(icd_p2,
file = paste0("output/files_2021_summer/icd_procedure_sc_vs_nosc_", yr, ".csv"))
rm(mc, icd_p2)
gc()
cat(paste0(yr, " done at ", Sys.time(), "\n"))
}
rm(icd_p)
gc()
## medical header
for(yr in 2013:2017){
cat(paste0("begin ", yr, " at ", Sys.time(), "\n"))
hd <- fread(paste0("E:/CT_APCD/Sai/intermediate_data/",
"cost_measure_intermediate_data/",
"medical_header_fiscalyear_", yr, ".csv"),
colClasses = "character")
mc <- fread(paste0("output/files_2021_summer/mc_sc_vs_nosc_", yr, ".csv"),
colClasses = "character",
select = c("MEDICAL_CLAIM_SERVICE_LINE_ID",
"MEDICAL_CLAIM_HEADER_ID",
"sc_pt_flag",
"pc_flag",
"ip_flag",
"op_flag" ))
hd <- hd[mc, on = "MEDICAL_CLAIM_HEADER_ID", nomatch = 0]
fwrite(hd,
file = paste0("output/files_2021_summer/medical_claim_header_sc_vs_nosc_", yr, ".csv"))
rm(mc, hd)
gc()
cat(paste0(yr, " done at ", Sys.time(), "\n"))
}
## pharmacy
for(yr in 2013:2017){
cat(paste0("begin ", yr, " at ", Sys.time(), "\n"))
phc <- rbindlist(lapply(yr:(yr - 1), function(x){
rt <- fread(paste0("E:/CT_APCD/Uconn_extract_20180521_12312017/PHARMACY_",
x, ".txt"),
colClasses = "character",
select = c("pharmacy_claim_service_line_id",
"INTERNAL_MEMBER_ID",
"SUBMITTER_ID",
"PRODUCT_CODE",
"prescription_filled_dt", "NATIONAL_DRUG_CODE",
"DRUG_NAME", "REFILL_NUMBER", "QUANTITY",
"DAYS_SUPPLY", "THIRTY_DAY_EQUIVALENT",
"CHARGE_AMT", "PAID_AMT", "COPAY_AMT",
"CLAIM_STATUS_CODE", "DENIED_CLAIM_FLAG",
"GENERIC_DRUG_IND_CODE"))[INTERNAL_MEMBER_ID %in% pt$INTERNAL_MEMBER_ID]
return(rt)
}))
phc <- phc[ymd(mdy(prescription_filled_dt)) >= ymd(paste0(yr - 1, '-10-01')) &
ymd(mdy(prescription_filled_dt)) <= ymd(paste0(yr, '-09-30'))]
mc <- fread(paste0("output/files_2021_summer/mc_sc_vs_nosc_", yr, ".csv"),
colClasses = "character",
select = c("MEDICAL_CLAIM_SERVICE_LINE_ID",
"INTERNAL_MEMBER_ID",
"sc_pt_flag",
"pc_flag",
"ip_flag",
"op_flag" ))
phc <- phc[mc, on = "INTERNAL_MEMBER_ID", nomatch = 0, allow.cartesian=TRUE]
fwrite(phc,
file = paste0("output/files_2021_summer/pharmacy_sc_vs_nosc_", yr, ".csv"))
rm(mc, phc)
gc()
cat(paste0(yr, " done at ", Sys.time(), "\n"))
}