Create NHS England CKD algorithm

Author: HeatherARobinson

NHS England CKD algorithm

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+#CKD IS STAGED HERE BASED ON MAINTENANCE OF EACH EGFR LEVEL FOR A MINIMUM OF 3 MONTHS
+#CKD HAS BEEN DERIVED HERE FROM CKD-EPI EGFR
+
+load("crea.repv12.rda") #table featuring 1 row per patient per day with maximum creatinine retained
+load ("sir.data.rda") #long format input file with 1 row per event entry
+
+#Reduce dataset to individuals eligible for CKD and AKI staging before looping;
+#Identify potential creatinine based CKD patients (individuals with any egfr<60)
+#Isolate the first qualifying test for each patient
+
+crea.rep$KDmarkE<-ifelse(!is.na(crea.rep$CKDEPIeGFR) & crea.rep$CKDEPIeGFR<60,1,0)
+CKsE<-crea.rep[crea.rep$KDmarkE==1,c("PatientID","EntryDate","KDmarkE")] #Kidney Injury flagged tests
+
+#Create a dataset including all data from patients with at least 1 KD flag:
+CKpotE<-crea.rep[crea.rep$PatientID %in% CKsE$PatientID,] 
+CKpotE$EntryDate2<-as.Date(as.character(CKpotE$EntryDate),format="%Y%m%d")
+
+#Mark a 90 day lookback period
+CKpotE$EntryDate1<-as.Date(as.character(CKpotE$EntryDate),format="%Y%m%d")-90
+CKpotE<-CKpotE[,c("PatientID","event.date","KDmarkE","EntryDate1","EntryDate2","CKDEPIeGFR")] 
+
+############################################################################################## CHECKED
+#Diagnose CKD
+#If eGFR under 60 is not sustained for 90 days, recode KDmark as 0
+for (i in 1:length(CKpotE$PatientID)){
+CKpotE$CKDE[i]<-min(crea.rep$KDmarkE[crea.rep$PatientID==CKpotE$PatientID[i] &
+crea.rep$event.date>CKpotE$EntryDate1[i] & crea.rep$event.date<=CKpotE$EntryDate2[i]])
+CKpotE$MaxCKDE[i]<-max(crea.rep$CKDEPIeGFR[crea.rep$PatientID==CKpotE$PatientID[i] &
+crea.rep$event.date>CKpotE$EntryDate1[i] & crea.rep$event.date<=CKpotE$EntryDate2[i]])
+}
+#CKD is 1 if the test qualifies and there is no normal test within 3 months prior
+#At this stage some are temporarily falsely positively identified that have no lookback test
+
+#Near date match EntryDate1 (90 days prior date)- to entries from the full dataset
+#neardate preferably matches to a prior entry if one is available
+#if the closest match is before EntryDate1 (data from more than 90 days prior available), retain row.
+indx1<-neardate(CKpotE$PatientID,crea.rep$PatientID,CKpotE$EntryDate1,crea.rep$event.date,best="prior",nomatch=NA_integer_)
+CKpotE$Lookback<-crea.rep[indx1,"event.date"]
+CKpotE$CKDGEStage<-ifelse(CKpotE$Lookback<=CKpotE$EntryDate1 & CKpotE$CKDE==1,1,0)
+CKpotE<-CKpotE[CKpotE$CKDGEStage==1,]
+#CKpot is a subset table of CKD qualifying tests and their markers to be merged onto crea.rep
+CKpotE<-unique(CKpotE)
+crea.rep<-merge(crea.rep,CKpotE[,c(1,2,8:10)],all.x=TRUE)
+crea.rep$CKDGEStage<-ifelse(!is.na(crea.rep$CKDGEStage),2,0)
+#Stage 1 is skipped here as it cannot be identified from creatinine only, start by coding all as stage 2
+table(crea.rep$CKDGEStage)
+
+crea.rep$CKDGEStage<-ifelse(crea.rep$CKDGEStage>0&crea.rep$MaxCKDE>=30&crea.rep$MaxCKDE<45,3.5,crea.rep$CKDGEStage)
+crea.rep$CKDGEStage<-ifelse(crea.rep$CKDGEStage>0&crea.rep$MaxCKDE>=45&crea.rep$MaxCKDE<60,3,crea.rep$CKDGEStage)
+crea.rep$CKDGEStage<-ifelse(crea.rep$CKDGEStage>0&crea.rep$MaxCKDE>=15&crea.rep$MaxCKDE<30,4,crea.rep$CKDGEStage)
+crea.rep$CKDGEStage<-ifelse(crea.rep$CKDGEStage>0&crea.rep$MaxCKDE<15,5,crea.rep$CKDGStage)
+crea.rep$CKDGEStage<-ifelse(is.na(crea.rep$CKDGEStage),0,crea.rep$CKDGEStage)
+table(crea.rep$CKDGEStage)
+
+#can replace with dplyr
+#Recode to KDIGO
+crea.rep$CKDGEStage<-ifelse(crea.rep$CKDGEStage==3.5,paste("3b"),paste(crea.rep$CKDGEStage))
+crea.rep$MaxCKDGEStage<-ifelse(crea.rep$MaxCKDGEStage==3.5,paste("3b"),paste(crea.rep$MaxCKDGEStage))
+
+
+#########################################################################################################
+
+#Mark start of first CKD diagnosis based on creatinine only
+CKs<-CKpot %>%
+group_by(PatientID)%>%
+slice(which.min(EntryDate1)) %>%
+as.data.frame
+CKs<-CKs[,c(1,2)]
+names(CKs)<-c("PatientID","CKDG_Date")
+crea.rep<-merge(crea.rep,CKs,all.x=TRUE)
+crea.rep$TimeSinceCKD<-difftime(as.Date(as.character(crea.rep$EntryDate),format="%Y%m%d"),crea.rep$CKDG_Date,unit="days")
+########################################################################################################
+
+#Incorporate Urine Albumin to creatinine ratio data if available:
+crea.rep$CKDAStage<-ifelse(crea.rep$UACratio<3,1,0)
+crea.rep$CKDAStage<-ifelse(crea.rep$UACratio>=3&crea.rep$UACratio<30&!crea.rep$CKDGStage=="0",2,crea.rep$CKDAStage)
+crea.rep$CKDAStage<-ifelse(crea.rep$UACratio>30&!crea.rep$CKDGStage=="0",3,crea.rep$CKDAStage)
+
+#Stage CKD based on both UAC and creatinine data:
+crea.rep$CKDGStage<-crea.rep$CKDGEStage
+crea.rep$CKDPrognosis<-crea.rep$CKDGStage
+crea.rep$CKDPrognosis<-ifelse(crea.rep$CKDGStage<=2 & crea.rep$CKDAStage==2,1,crea.rep$CKDPrognosis)
+crea.rep$CKDPrognosis<-ifelse(crea.rep$CKDGStage<=2 & crea.rep$CKDAStage==3,2,crea.rep$CKDPrognosis)
+crea.rep$CKDPrognosis<-ifelse(crea.rep$CKDGStage>=3,3,crea.rep$CKDPrognosis)
+crea.rep$CKDPrognosis<-ifelse(crea.rep$CKDGStage==3.5 & crea.rep$CKDAStage==1,2,crea.rep$CKDPrognosis)
+crea.rep$CKDPrognosis<-ifelse(crea.rep$CKDGStage==3 & crea.rep$CKDAStage==1,1,crea.rep$CKDPrognosis)
+crea.rep$CKDPrognosis<-ifelse(crea.rep$CKDGStage==3 & crea.rep$CKDAStage==2,2,crea.rep$CKDPrognosis)
+
+#Where CKD diagnosed based on creatinine, add metric for summarised eGFR range for further phenotyping
+crea.rep$CustomeGFR<-ifelse(crea.rep$CKDPrognosis>0 &crea.rep$MDRDeGFR>=60 & crea.rep$MDRDeGFR<90,1,NA)
+crea.rep$CustomeGFR<-ifelse(crea.rep$CKDPrognosis>0 & crea.rep$MDRDeGFR>=60 & crea.rep$MDRDeGFR<90,1,NA)
+crea.rep$CustomeGFR<-ifelse(crea.rep$CKDPrognosis>0 &crea.rep$MDRDeGFR>=45 & crea.rep$MDRDeGFR<60,2,crea.rep$CustomeGFR)
+crea.rep$CustomeGFR<-ifelse(crea.rep$CKDPrognosis>0 &crea.rep$MDRDeGFR>=30 & crea.rep$MDRDeGFR<45,3,crea.rep$CustomeGFR)
+crea.rep$CustomeGFR<-ifelse(crea.rep$CKDPrognosis>0 &crea.rep$MDRDeGFR>=15 & crea.rep$MDRDeGFR<30,4,crea.rep$CustomeGFR)
+crea.rep$CustomeGFR<-ifelse(crea.rep$CKDPrognosis>0 &crea.rep$MDRDeGFR<15,5,crea.rep$CustomeGFR)
+
+
+###################################################################################