This determines the follow up rule a patient should fit in to (according to the British Society for Gastroenterology guidance on Barrett's oesophagus) Specfically it combines the presence of intestinal metaplasia with Prague score so the follow-up group can be determined. It relies on the presence of a Prague score. It should be run after Barretts_PathStage which looks for the worst stage of a specimen and which will determine the presence or absence of intestinal metaplasia if the sample is non-dysplastic. Being the procedure done at the time and the follow-up timings

Barretts_FUType(dataframe, EndoReportColumn)

Arguments

dataframe

the dataframe(which has to have been processed by the Barretts_PathStage function first to get IMorNoIM),

EndoReportColumn

The field to search (endoscopic findings)

Examples

# 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 default
v<-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: b<-Barretts_PathStage(v,'Histology') b2<-Barretts_EventType(b,'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. cc<-Barretts_FUType(b2,'Findings') rm(v)