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
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")
#> Warning: argument is not an atomic vector; coercing
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")
#> Warning: There were 6 warnings in `mutate()`.
#> The first warning was:
#> ℹ In argument: `FU_Type = case_when(...)`.
#> Caused by warning:
#> ! NAs introduced by coercion
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 5 remaining warnings.
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"
)
#> Warning: NAs introduced by coercion
#> Warning: NAs introduced by coercion
rm(v)