View source: R/Module_Barretts.R
BarrettsBxQual | R Documentation |
This function gets the number of biopsies taken per endoscopy and compares it to the Prague score for that endoscopy.Endoscopists should be taking a certain number of biopsies given the length of a Barrett's segment so it should be straightforward to detect a shortfall in the number of biopsies being taken. The output is the shortfall per endoscopist
BarrettsBxQual(dataframe, Endo_ResultPerformed, PatientID, Endoscopist)
dataframe |
dataframe |
Endo_ResultPerformed |
Date of the Endoscopy |
PatientID |
Patient's unique identifier |
Endoscopist |
name of the column with the Endoscopist names |
Other Disease Specific Analysis - Barretts Data:
BarrettsAll()
,
BarrettsParisEMR()
,
Barretts_FUType()
,
Barretts_PathStage()
,
Barretts_PragueScore()
# Firstly relevant columns are extrapolated from the # Mypath demo dataset. These functions are all part of Histology data # cleaning as part of the package. Mypath$NumBx <- HistolNumbOfBx(Mypath$Macroscopicdescription, "specimen") Mypath$BxSize <- HistolBxSize(Mypath$Macroscopicdescription) # The histology is then merged with the Endoscopy dataset. The merge occurs # according to date and Hospital number v <- Endomerge2( Myendo, "Dateofprocedure", "HospitalNumber", Mypath, "Dateofprocedure", "HospitalNumber" ) # The function relies on the other Barrett's functions being run as well: b1 <- Barretts_PragueScore(v, "Findings") b1$PathStage <- Barretts_PathStage(b1, "Histology") # The follow-up group depends on the histology and the Prague score for a # patient so it takes the processed Barrett's data and then looks in the # Findings column for permutations of the Prague score. b1$FU_Type <- Barretts_FUType(b1, "CStage", "MStage", "PathStage") colnames(b1)[colnames(b1) == "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( b1, "Date.x", "HospitalNumber", "Endoscopist" ) rm(v)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.