This function gets the biopsies taken per endoscopy and compares to the Prague score for that endoscopy.
BarrettsBxQual(dataframe, Endo_ResultPerformed, PatientID, Endoscopist)
dataframe | dataframe |
---|---|
Endo_ResultPerformed | Date of the Endocscopy |
PatientID | Patient's unique identifier |
Endoscopist | name of the column with the Endoscopist names |
# Firstly relevant columns are extrapolated from the # Mypath demo dataset. These functions are all part of Histology data # cleaning as part of the package. v<-HistolDx(Mypath,'Diagnosis') v<-HistolExtrapolDx(v,'Diagnosis')#> Error in paste0("[Cc]arcin|[Cc]ance|[Ll]ymphoma|[Tt]umour|[Dd]yspla|G[Ii][Ss][Tt]|[Ss]tromal|[Ll]eio|[Cc]rohn", userString): argument "userString" is missing, with no defaultv<-HistolNumbOfBx(v,'Macroscopicdescription','specimen') v<-HistolBxSize(v,'Macroscopicdescription') # The histology is then merged with the Endoscopy dataset. The merge occurs # according to date and Hospital number v<-Endomerge2(Myendo,'Dateofprocedure','HospitalNumber',v,'Dateofprocedure', 'HospitalNumber') # The function relies on the other Barrett's functions being run as well: b1<-Barretts_PragueScore(v,'Findings') b2<-Barretts_PathStage(b1,'Histology') b3<-Barretts_EventType(b2,'Histology','ProcedurePerformed', 'Indications','Findings') # The follow-up group depends on the histology and the Prague score for a # patient so it takes the processed Barrett's data and then looks in the # Findings column for permutations of the Prague score. b4<-Barretts_FUType(b3,'Findings') colnames(b4)[colnames(b4) == 'pHospitalNum'] <- 'HospitalNumber' # The number of average number of biopsies is then calculated and # compared to the average Prague C score so that those who are taking # too few biopsies can be determined hh<-BarrettsBxQual(b4,'Date.x','HospitalNumber', 'Endoscopist') rm(v)