Package index

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.