Function 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

NegativeRemoveWrapper(): Wrapper for Negative Remove

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

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

PatientFlowIndividual(): Create a plot over time of patient categorical findings as a line chart

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.