collapse_pharmacy_long_vs.R

################################################################################
### collapse medical diagnosis intermediate file
### version controlled by git
################################################################################

## setup tools and packages
library(methods)
source("E:/CT_APCD/gitrepo/ct-apcd/R/utils.R")
need_pkgs <- c("data.table", "bit64", "tools", "dplyr")
need.packages(need_pkgs)
source("functions.R")
source("docs.R")


## directory of raw data and output
inDir <- input_dir("E:/CT_APCD/Sai/lds2021/lds2021file/value_sets/pharmacy/")
outDir <- output_dir("E:/CT_APCD/Sai/lds2021/lds2021file/value_sets/pharmacy_long/")
load("E:/CT_APCD/shared/intermediate_data/APCD_modified/hedis/phar.long.regexp.rda")
vs.long[2, 1] <- "ACE Inhibitor ARB Medications"
vs.long[15, 1] <- "Potentially Harmful Drugs—Rate 1 and Rate 2 Medications"
vs.long[16, 1] <- "Potentially Harmful Drugs—Rate 1 Medications"
vs.long[17, 1] <- "Potentially Harmful Drugs—Rate 2 Medications"
## processing
for(year in 2019:2019){
 for (vs_i in vs.long$`Value Set Name`){
    vs.tmp <- filter(vs.long, `Value Set Name` %in% vs_i)
    tmp <- strsplit(vs.tmp$code_regexp, split='|', fixed=T)[[1]]
    n.chunk <- ceiling(length(tmp) / 500)
    fdir <- paste0(inDir, "pharmacy_", year, "#national_drug_code#",
        vs_i,  " ", sprintf("%01d", 1:n.chunk), ".csv")
    for (fdir_i in fdir){
        f_i <- fread(fdir_i, header = TRUE, colClasses = 'character', encoding = 'UTF-8')
        fwrite(f_i, paste0(outDir, "pharmacy_", year, "#national_drug_code#", vs_i, ".csv"), append = TRUE)
        cat(paste0(fdir_i, " done!\n"))
    }
    Sys.time()
 }
}