BarrettsBxQual: Barrett's number of biopsies

In sebastiz/EndoMineR_devlop: Functions to mine endoscopic and associated pathology datasets

Description

This function gets the biopsies taken per endoscopy and compares to the Prague score for that endoscopy.

Usage

BarrettsBxQual(dataframe, Endo_ResultPerformed, PatientID, Endoscopist)

Arguments

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

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)

sebastiz/EndoMineR_devlop documentation built on May 29, 2019, 7:33 a.m.