drug utilization assessment 22 Oct

#Drug utilization assessment
library(tidyverse)
library(readxl)
library(dplyr)
library(lubridate)
library(doBy)
library(plyr)
library(readr)     
library(frequency)   
library(DescTools)
library(purrr)
library(rJava)
library(xlsx)
library(dostats)

setwd("E:/Ningbo Projects/TB/TB project/Workingd/CSV files/")
Sys.setlocale(category = "LC_ALL",local="chinese")
IPT<-read_csv("IPT_TB_1021.csv")
OPT<-read_csv("OPT_TB_1021.csv")
id_list<-read_csv("id_list_1021morning.csv")
IPT_pharm<-read_csv("IPT_pharm.csv")
OPT_pharm<-read_csv("OPT_pharm.csv")

#load all drug list files
IPT_pharm_list<-read_xlsx("iptdrugbook.xlsx")
OPT_pharm_list<-read_xlsx("optdrugbook.xlsx")

IPT_pharm_list$Cat[IPT_pharm_list$Cat=="TCM" & grepl("注射",IPT_pharm_list$level)]<-"TCM_inj"
OPT_pharm_list$Cat[OPT_pharm_list$Cat=="TCM" & grepl("注射",OPT_pharm_list$level)]<-"TCM_inj"

#Merge drug types to the OPT and IPT pharm lists;
IPT_pharm_index<- inner_join(IPT_pharm ,IPT_pharm_list, by = c("item_name" = "level"))
OPT_pharm_index<- inner_join(OPT_pharm ,OPT_pharm_list, by = c("item_name" = "level"))
OPT_pharm_index$Cat[OPT_pharm_index$Cat=="TB"]<-"anti_tuberculosis"
table(OPT_pharm_index$Cat)
write_excel_csv(IPT_pharm_index,"IPT_pharm_1021.csv")
write_excel_csv(OPT_pharm_index,"OPT_pharm_1021.csv")

#prepare for GEE file in ipt assessment
IPT_outcome<-read_csv("ipt_outcome.csv")
IPT_all<- inner_join(IPT ,IPT_outcome, by = c("idcard" = "idcard","adm_time" = "adm_time" ))
library(gee)

summary(gee(N_Hepato ~ as.factor(tier), id=idcard, data=IPT_all, family = poisson, corstr="exchangeable"))

OPT_outcome<-read_csv("opt_outcome.csv")
OPT_all<- inner_join(OPT ,OPT_outcome, by = c("idcard" = "idcard","clinic_time" = "clinic_time" ))
library(geepack)
OPT_all_temp<-OPT_all[OPT_all$tier=="tier_3" & !OPT_all$org_name=="慈溪市妇幼保健院" & !OPT_all$org_name=="慈溪市人民医院" &
                       !OPT_all$org_name=="宁海县妇幼保健院" & !OPT_all$org_name=="宁波市精神病院",]

id_list_index<-id_list %>% select(idcard, Sex,age)
IPT_all<- inner_join(IPT_all ,id_list_index, by = c("idcard" = "idcard" ))
OPT_all<- inner_join(OPT_all ,id_list_index, by = c("idcard" = "idcard" ))

write_excel_csv(IPT_all,"IPT_analytical_1022.csv")
write_excel_csv(OPT_all,"OPT_analytical_1022.csv")

table(IPT_all$org_name)
IPT_temp<-IPT_all[ IPT_all$org_name=="鄞州二院" 
                  | IPT_all$org_name=="宁波市第一医院" | IPT_all$org_name=="宁波市第九医院" 
                  | IPT_all$org_name=="宁波市北仑区人民医院", ]
mf <- formula(N_Hepato ~ as.factor(org_name))
gee1 <- geeglm(mf, data=IPT_temp, id=idcard, family=poisson, corstr="exchangeable")
gee1