Standardises the location of biopsies by cleaning up the common typos and abbreviations that are commonly used in free text of pathology reports

TermStandardLocation(dataframe, SampleLocation)

Arguments

dataframe

The dataframe

SampleLocation

Column describing the Macroscopic sample from histology

Examples

#Firstly we extract histology from the raw report # using the extractor function mywords<-c("Hospital Number","Patient Name:","DOB:","General Practitioner:", "Date received:","Clinical Details:","Macroscopic description:", "Histology:","Diagnosis:") MypathExtraction<-Extractor(PathDataFrameFinal,"PathReportWhole",mywords) names(MypathExtraction)[names(MypathExtraction) == 'Datereceived'] <- 'Dateofprocedure' MypathExtraction$Dateofprocedure <- as.Date(MypathExtraction$Dateofprocedure) # The function then standardises the histology terms through a series of # regular expressions ll<-TermStandardLocation(Mypath,'Histology') rm(MypathExtraction)