This looks at the Paris grades of each EMR and then creates a heatmap of pathological grade vs endoscopic Paris grade.This should only be run after all the BarrettsDataAccord functions.

BarrettsParisEMR(EndoSubsetEMR, Column, Column2)

Arguments

EndoSubsetEMR

The dataframe

Column

Endoscopy report field of interest

Column2

Another endoscopy report field of interest

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<-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 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: 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 function compares the Paris score # from the endoscopy report free text to # the histopathology scores for the same endoscopies so you can see what the # lesion recognition is like overall mm<-BarrettsParisEMR(b4,"ProcedurePerformed","Findings") rm(v)