This function extracts the Event- usually a therapeutic event, from the text eg endoscopic mucosal resection, radiofrequency ablation etc. It does not currently include stricture dilatation.Specfically it extracts the event
Barretts_EventType(dataframe, HistolReportColumn, ProcPerformedColumn, EndoReportColumn, EndoFindingsColumn)
dataframe | the dataframe |
---|---|
HistolReportColumn | The histology main text |
ProcPerformedColumn | The Procedure Performed column |
EndoReportColumn | The endoscopic diagnosis column |
EndoFindingsColumn | The endoscopic findings column if different to the Diagnosis column |
# 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<-HistolAccessionNumber(Mypath,'Histology', 'SP-\\d{2}-\\d{7}') v<-HistolDx(v,'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 then looks within the Histology and the # Procedure performed, free text endoscopic Findings and the original # whole endoscopy report columns from the merged data set (v) for # EMR/APC/RFA/HALO so that the event for the procedure, is recorded. bb<-Barretts_EventType(v,'Histology', 'ProcedurePerformed','Indications','Findings') rm(v)