Determine the Follow up group

This determines the follow up rule a patient should fit in to (according to the British Society for Gastroenterology guidance on Barrett's oesophagus) Specfically it combines the presence of intestinal metaplasia with Prague score so the follow-up group can be determined. It relies on the presence of a Prague score. It should be run after Barretts_PathStage which looks for the worst stage of a specimen and which will determine the presence or absence of intestinal metaplasia if the sample is non-dysplastic. Because reports often do not record a Prague score a more pragmatic approach as been to assess the M stage and if this is not present then to use the C stage extrapolated using the Barretts_Prague function

Usage

Barretts_FUType(dataframe, CStage, MStage, IMorNoIM)

Arguments

dataframe

the dataframe(which has to have been processed by the Barretts_PathStage function first to get IMorNoIM and the Barretts_PragueScore to get the C and M stage if available),

CStage

CStage column

MStage

MStage column

IMorNoIM

IMorNoIM column

See also

Other Disease Specific Analysis - Barretts Data: BarrettsAll(), BarrettsBxQual(), BarrettsParisEMR(), 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 demo dataset. These functions are all part of Histology data
# cleaning as part of the package.
v <- Mypath
v$NumBx <- HistolNumbOfBx(v$Macroscopicdescription, "specimen")
v$BxSize <- HistolBxSize(v$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:
v$IMorNoIM <- Barretts_PathStage(v, "Histology")
v <- Barretts_PragueScore(v, "Findings")
#> Warning: argument is not an atomic vector; coercing

# 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.
v$FU_Type <- Barretts_FUType(v, "CStage", "MStage", "IMorNoIM")
#> 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.
rm(v)