Analysis

A fundamental design principle of EndoMineR was that it should address the important categories of questions we all have in gastroenterology, and endoscopy in particular. These questions roughly fall into the following: surveillance, quality and also operational questions (eg patient flow through endoscopy).

##1. Surveillance functions

Surveillance tracking is difficult because it relies on assessment at several timepoint and then deciding on the next examination based on a ruleset. A basic question is often: ’How good are our surveillance programmes?” which really means “How good are we at making sure patients come back in a timely way for their endoscopy after a polyp removal or for Barrett’s surveillance”, for example?

Surveillance relates to the timing of a test relative to other tests or all tests done for a patient. To do this, the EndoMineR surveillance functions simply order the endoscopies by patient and date, and extract the date the first test was done, as well as the last test (of the same type) and the difference in timing between each test, always grouped by patient.

As all these functions are simply looking at the date of the test, they can take a raw dataset, as long as a date column is present and use that, rather than have a lot of pre-processing steps. Of course, the pre-processing steps explained in the EndoMineR vignette (mainly using the textPrep function) are recommended however as then the user will be able to perform any other additional analyses if needed.

The basic surveillance functions are simple but are the most used. SurveilTimeByRow will extract the time difference between each individual endoscopy for an individual patient. This is useful to see how adherent the surveillance endoscopy is to guidelines.

SurveilLastTest simply extracts the last and first test respectively for each patient so you can assess how long the patient has been surveilled for. This is likely to come in useful for future iterations of EndoMineR as patient Theographs are developed (work in progress).

em1<-SurveilTimeByRow(Myendo,'HospitalNumber','Dateofprocedure')

em3<-SurveilLastTest(Myendo,'HospitalNumber','Dateofprocedure')

em4<-SurveilFirstTest(Myendo,'HospitalNumber','Dateofprocedure')

Of course we may also want to know how many tests have been done over a time period and this is provided by the function HowManyTests

This function will return the number of tests by day, month and year so they can be easily graphed according to what you want.

how<-HowManyOverTime(Myendo,'Indications','Dateofprocedure','Surv')

library(tm)
myNotableWords <- c("barrett", "coeliac")
ListLookup(Myendo,'Findings',myNotableWords)

##        X2  Prop
## 1 barrett 18.05
## 2 coeliac  6.20

#We have to attach the output of EndoscMeds to the original dataframe
MyendoNew<-cbind(EndoscMeds(Myendo$Medications),Myendo)
#Average Fentanyl use by endoscopist:
Mytable<-MetricByEndoscopist(MyendoNew,'Endoscopist','Fent')

#how<-SurveySankey(Myendo,"ProcedurePerformed")

#flow<-PatientFlow_CircosPlots(v,"Date.y","pHospitalNum","ProcedurePerformed")