BarrettsBxQual: Get the number of Barrett's biopsies taken

In ropensci/EndoMineR: Functions to mine endoscopic and associated pathology datasets

Get the number of Barrett's biopsies taken

Description

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

Usage

BarrettsBxQual(dataframe, Endo_ResultPerformed, PatientID, Endoscopist)

Arguments

dataframe	dataframe
Endo_ResultPerformed	Date of the Endoscopy
PatientID	Patient's unique identifier
Endoscopist	name of the column with the Endoscopist names

See Also

Other Disease Specific Analysis - Barretts Data: BarrettsAll(), BarrettsParisEMR(), Barretts_FUType(), Barretts_PathStage(), Barretts_PragueScore()

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.
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)

ropensci/EndoMineR documentation built on March 14, 2023, 3:58 a.m.