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
Barretts_FUType(dataframe, CStage, MStage, IMorNoIM)
| 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 |
Other Disease Specific Analysis - Barretts Data:
BarrettsAll(),
BarrettsBxQual(),
BarrettsParisEMR(),
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 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: NAs introduced by coercion#> Warning: NAs introduced by coercion#> Warning: NAs introduced by coercion#> Warning: NAs introduced by coercion#> Warning: NAs introduced by coercion#> Warning: NAs introduced by coercionrm(v)