Reference

NLP - Text Cleaning and Extraction:

Functions to clean raw text

textPrep()

Combine all the text cleaning and extraction functions into one

Extractor()

Extract columns from the raw text

DictionaryInPlaceReplace()

Dictionary In Place Replace

NegativeRemove()

Remove negative and normal sentences

spellCheck()

Find and Replace

ColumnCleanUp()

Tidy up messy columns

ListLookup()

Extract from report, using words from a list

NLP - Text merging:

Functions to help merge datasets

EndoPaste()

Paste endoscopy and histology results into one

Endomerge2()

Merge endoscopy and histology data.

NLP - Lexicons:

Basic lexicons

HistolType()

Use list of pathology types

LocationList()

Use list of upper and lower GI standard locations

LocationListUpper()

Use list of standard locations for upper GI endoscopy

LocationListUniversal()

Use list of standard locations for upper GI endoscopy

LocationListLower()

Use list of standard locations for lower GI endoscopy

RFACath()

Use list of catheters used in radiofrequency ablation

EventList()

Use list of endoscopic events and procedures

BiopsyIndex()

Index biopsy locations

GISymptomsList()

Index of GI symptoms

WordsToNumbers()

Convetr words to numbers especially for the histopathology text

Basic Column mutators

Basic Column mutators

ExtrapolatefromDictionary()

Extrapolate from Dictionary

ListLookup()

Extract from report, using words from a list

EntityPairs_OneSentence()

See if words from two lists co-exist within a sentence

EntityPairs_TwoSentence()

Look for relationships between site and event

MyImgLibrary()

Clean html endoscopic images

Specific Text Cleaning - Endoscopy specific cleaning functions:

Functions to help clean endoscopy reports

EndoscEndoscopist()

Clean endoscopist column

EndoscInstrument()

Clean instrument column

EndoscMeds()

Clean medication column

EndoscopyEvent()

Extract the endoscopic event.

Specific Text Cleaning - Histology specific cleaning functions:

Functions to help clean histology text

HistolNumbOfBx()

Extract the number of biopsies taken from the histology report

HistolBxSize()

Determine the largest biopsy size from the histology report

HistolTypeAndSite()

Extract the site a specimen was removed from as well as the type

Basic Analysis Helper - Grouping by endoscopist

Grouping by endoscopist

MetricByEndoscopist()

Plot a metric by endoscopist

CategoricalByEndoscopist()

Group anything by Endoscopist and returns the table

Basic Analysis - Surveillance Functions:

Functions to analyse surveillance intervals

SurveilTimeByRow()

Extract the time difference between each test in days

SurveilLastTest()

Extract the last test done by a patient only

SurveilFirstTest()

Extracts the first test only per patient

TimeToStatus()

Extract the time to an event

HowManyOverTime()

Number of tests done per month and year by indication

Disease Specific Analysis - Barretts Data

Functions for reading and writing Barretts Data.

BarrettsAll()

Run all the basic Barrett's functions

BarrettsBxQual()

Get the number of Barrett's biopsies taken

BarrettsParisEMR()

Run the Paris classification versus worst histopath grade for Barrett's

Barretts_FUType()

Determine the Follow up group

Barretts_PathStage()

Get the worst pathological stage for Barrett's

Barretts_PragueScore()

Extract the Prague score

Disease Specific Analysis - Polyp functions:

Polyp analysis

GRS_Type_Assess_By_Unit()

Create GRS metrics by endoscopist (X-ref with pathology)

Patient Flow functions:

Visualise patient flow

SurveySankey()

Create a Sankey plot for patient flow

PatientFlow_CircosPlots()

Create a Circos plot for patient flow

Data overview:

Basic consort diagrams

sanity()

Create a basic consort diagram from dataframes

Data Presentation helpers:

Functions to help with data visualisation

theme_Publication()

Set the publication theme for all the ggplots

scale_fill_Publication()

Set the fills for all the ggplots

scale_colour_Publication()

Set the colour theme for all the ggplots

EndoBasicGraph()

Basic graph creation using the template specified in theme_Publication.