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')| HospitalNumber | TimeSinceLast |
|---|---|
| A1648588 | 3270 days |
| A1648588 | 3270 days |
| A1648588 | 3270 days |
| A1648588 | 3270 days |
| A1648588 | 3270 days |
em3<-SurveilLastTest(Myendo,'HospitalNumber','Dateofprocedure')| HospitalNumber | Dateofprocedure |
|---|---|
| J1337672 | 2013-03-25 |
| Q7176341 | 2014-05-31 |
| M5148114 | 2014-06-18 |
| Q7729897 | 2014-07-19 |
| R3882435 | 2014-11-15 |
em4<-SurveilFirstTest(Myendo,'HospitalNumber','Dateofprocedure')| HospitalNumber | Dateofprocedure |
|---|---|
| F7957976 | 2001-01-03 |
| Y8594667 | 2001-01-04 |
| Z6299612 | 2001-01-08 |
| R8004923 | 2001-01-15 |
| U1759838 | 2001-01-16 |
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')| day | week | month | year | freq | MonthYear |
|---|---|---|---|---|---|
| 25 | 4 | 1 | 2001 | 1 | 2001-01-01 |
| 27 | 4 | 1 | 2001 | 1 | 2001-01-01 |
| 23 | 12 | 3 | 2001 | 1 | 2001-03-01 |
| 11 | 15 | 4 | 2001 | 1 | 2001-04-01 |
| 20 | 16 | 4 | 2001 | 1 | 2001-04-01 |
2. Assessment of quality functions
Quality is measured in a variety of ways. For endoscopy it is measured according to the adherence to a) standards for endoscopic documentation as well as b) detection of certain pathological conditions such as dysplasia (best summarised as lesion recognition)
a) Documentation Quality
As regards adherence to documentation for example, a generic function is provided that will look up the presence of words presented in a list in a target column. It will then output the proportion of reports that have these words, as well as a barchart to show what proportion of the endoscopies showed these words. The list can be comprised of terms that should be mentioned in a report.
Input
| HospitalNumber | PatientName | Findings |
|---|---|---|
| J6044658 | Jargon, Victoria | No evidence of Barrett’s oesophagus, short 2 cn hiatus hernia ,Oesophageal biopsies taken from three levels as requested ,OGD today to assess for ulceration/ongoing bleeding ,Diaphragmatic pinch:40cm ,She has a small hiatus hernia ,We will re-book for 2 weeks, rebanding ,Tiny erosions at the antrum ,Biopsies taken from top of stricture-metal marking clips in situ ,The varices flattened well with air insufflation ,He is on Barrett’s Screeling List in October 2017 at St Thomas’ HALO 90 done with good effect |
| Y6417773 | Powell, Destiny | Duodenum: Duodenitis with a small erosion ,STOMACH: diffuse gastritis with angiodysplasia and punctate bleeding site on greater curve mid body - no obvious ulcer- antrum scar ?,No immediate complications ,Z-line at: 38cm - Bravo placed at 32cm- good positionat check endoscopy |
| B6072011 | Martinez-Santos, Ana | Stomach- Body Polyp- Pedunculated ,Several erosions/small ulcers in inflammed antrum ,Lax cardia with small hiatus hernia but no erosive oesophagitis ,DUODENUM: Normal to D3 |
| G1449886 | Lopez, Maria | STOMACH: Small amount of bright red blood that seems to have refluxed back through the pylorus |
| V1607560 | al-Rahimi, Rif’a | Coffee ground vomit ,OESOPHAGUS: the previous subepithelial lesion measuring 1 TTS HALO to area |
| I8031481 | Forrest, Dazheea | Stomach- Pylorus ,No cervical inlet patch |
In this example we are looking for the words Barrett’s and coeliac as perhaps we have chosen the macroscopic recognition of these features to denote what an endoscopist should always describe in the endoscopy report:
library(tm)
myNotableWords <- c("barrett", "coeliac")
ListLookup(Myendo,'Findings',myNotableWords)## X2 Prop
## 1 barrett 18.05
## 2 coeliac 6.20So we can see that the terms are present in the minority of reports across endoscopists, so perhaps we can look into this further..
b) Endoscopic Quality
Sedation Usage
Another measure of quality is the assessment of those factors that are recorded at endoscopy such as degree of sedation used etc. Rather than provide a function for each metric, again a generic function is provided that uses any quantifiable metric and plots it against the endoscopist. This function returns a list with two elements- the plot and the table:
#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')| MyendoNew.Endoscopist | MyendoNew.Fent |
|---|---|
| Dr Sullivan, Shelby | NA |
| Dr Kekich, Annabelle | 125 |
| Dr Sullivan, Shelby | 125 |
| Dr Avitia-Ramirez, Alondra | NA |
| Dr Greimann, Phoua | 75 |
| Dr Avitia-Ramirez, Alondra | 150 |
| Dr Martinez, Maegen | 125 |
| Dr Anderson, Alana | 75 |
| Dr Anderson, Alana | 25 |
| Dr Ives, Rashiah | 150 |
4.Patient flow functions
Sankey plots
We often like to get an overview of how patients are flowing through a system overall. This can give a nice visual representation of whether which patients diverge from the normal flow through a system so we can study them further. There are two ways to look at this. Sankey plots give good timepoint by timepoint representation of flow. This really works with more than one type of event at each timepoint.
For example, if we have a dataset with events such as ‘radiofrequency ablation’ and ‘endoscopic mucosal resection’ or ‘nothing’ we can use the Sankey plot to determine the order of events over a large patient population. You choose the column in the dataframe that describes the Procedure type (“EMR”,“RFA”,“nothing” in this case)
#how<-SurveySankey(Myendo,"ProcedurePerformed")
Circos plots
We may need something even more aggregated. Perhaps we want to see the overall number of patients that go from one event to another regardless of which timepoint it is at. To do this we can use a circos plot, which makes use of the circlize library, as follows:
#flow<-PatientFlow_CircosPlots(v,"Date.y","pHospitalNum","ProcedurePerformed")