TB case identification 2 Oct

library(tidyverse)
library(readxl)
library(dplyr)
library(lubridate)
library(doBy)
library(plyr)
library(readr)     
library(frequency)   
library(DescTools)
library(purrr)
library(rJava)
library(xlsx)


# TB case from OPT Pharm
setwd("E:/Ningbo Projects/TB/TB project/Raw data/OPT_pharm/")
ldf <- list() # creates a list
listxlsx <- dir(pattern = "*.xlsx") # creates the list of all the xlsx files in the directory
OPT_pharm <- ldply(listxlsx, read_xlsx)

TB_OPT_pharm<-filter(OPT_pharm, grepl("结核",disease_name))
TB_OPT_pharm$TB_time<-TB_OPT_pharm$clinic_time

#TB case from OPT file
setwd("E:/Ningbo Projects/TB/TB project/Raw data/OPT/")
ldf <- list() # creates a list
listxlsx <- dir(pattern = "*.xlsx") # creates the list of all the xlsx files in the directory
OPT<- ldply(listxlsx, read_xlsx)

TB_OPT<-filter(OPT, grepl("结核",disease_name))
TB_OPT$TB_time<-TB_OPT$clinic_time

#IPT_pharm cleaning

setwd("E:/Ningbo Projects/TB/TB project/Raw data/IPT_pharm/")
ldf <- list() # creates a list
listxlsx <- dir(pattern = "*.xlsx") # creates the list of all the csv files in the directory
IPT_pharm <- ldply(listxlsx, read_xlsx)


#TB case from IPT file
setwd("E:/Ningbo Projects/TB/TB project/Raw data/IPT/")
ldf <- list() # creates a list
listxlsx <- dir(pattern = "*.xlsx") # creates the list of all the xlsx files in the directory
IPT<- ldply(listxlsx, read_xlsx)

TB_IPT<-filter(IPT, grepl("结核",disease_name))
TB_IPT$TB_time<-TB_IPT$dis_time

#Lab results cleaning
setwd("E:/Ningbo Projects/TB/TB project/Raw data/Raw data/Lab/")
ldf <- list() # creates a list
listxlsx <- dir(pattern = "*.xlsx") # creates the list of all the csv files in the directory
Lab <- ldply(listxlsx, read_xlsx)
Lab$result_num<-as.numeric(Lab$result)

#Merge all files on TB diagnosis
TB_all<-gtools::smartbind(TB_OPT_pharm,TB_OPT,TB_IPT)

summary_TB<-TB_all %>% 
  group_by(idcard)  %>% 
  summarise_at(vars(TB_time), min, na.rm = TRUE)

#liver injury by diagnosis codes
Case_OPT_pharm<-filter(OPT_pharm, grepl("肝",disease_name))
Case_OPT_pharm$Case_time<-Case_OPT_pharm$clinic_time

Case_OPT<-filter(OPT, grepl("肝",disease_name))
Case_OPT$Case_time<-Case_OPT$clinic_time

Case_IPT<-filter(IPT, grepl("肝",disease_name))
Case_OPT$Case_time<-Case_OPT$clinic_time

Case_all<-gtools::smartbind(Case_OPT_pharm,Case_OPT,Case_IPT)
#export files
setwd("E:/Ningbo Projects/TB/TB project/Workingd/")
write_xlsx(Case_all, file = "liver_dx.xlsx", sheetName = "Liver_Dx_file")
write_xlsx(TB_all, file = "TB_dx.xlsx", sheetName = "TB_Dx_file")
write.xlsx(IPT, file = "IPT.xlsx", sheetName = "IPT_file")
write_xlsx(OPT, file = "OPT.xlsx", sheetName = "OPT_file")
write_xlsx(IPT_pharm, file = "IPT_pharm.xlsx", sheetName = "IPT_pharm_file")
write_xlsx(OPT_pharm, file = "OPT_pharm.xlsx", sheetName = "OPT_pharm_file")

write_xlsx(Lab, file = "Lab.xlsx", sheetName = "Lab_file")

DILI_all<-filter(Case_all, grepl("药物性",disease_name))
DILI_all<-filter(Case_all, grepl("",disease_name))