All functions

BarrettsAll

Follow up group determination

BarrettsBasicNumbers

Barretts Basic Numbers

BarrettsBxQual

Barrett's number of biopsies

Barretts_CRIM

CRIM status Barrett's

BarrettsDDRQual

Dysplasia detection rate on surveillance

BarrettsDocumentQual

Analysis of Barrett's Documentation Quality

BarrettsEMRGrades

Number of Barrett's EMRs by grade

Barretts_EventType

Therapeutic subtypes

Barretts_FUType

Follow up group determination

BarrettsParisEMR

Paris vs histopath Barrett's

BarrettsPathDetectQual

Dysplasia detection on surveillance

Barretts_PathStage

Worst pathological stage Barrett's

Barretts_PragueScore

Prague score extraction

BarrettssRFACath

RFA catheter use

BarrettsSurveil_HospNum

Unique Hospital Numbers of Barrett's patients

BarrettsSurveil

How many Barrett's patients had surveillance

ColonFinal

Fake Lower GI Endoscopy Set

ColumnCleanUpAll

Tidies up all columns

ColumnCleanUp

Tidies up messy columns

Endomerge2

Endomerge

EndoMineR

EndoMineR: A package for analysis of endoscopic and related pathology

EndoscAll

Extracts the columns from the raw report

EndoscEndoscopist

Cleans endoscopist column if present

EndoscFindings

Cleans Procedure performed column if present

EndoscIndications

Cleans indications column if present

EndoscInstrument

Cleans instrument column if present

EndoscMeds

Cleans medication column if present

EndoscProcPerformed

Cleans Procedure performed column if present

Extractor

Extracts the columns from the raw report

GRS_Type_Assess_By_Unit

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

HistolAccessionNumber

Extract histological accession number

HistolAll

Clean up all Histology data

HistolBxSize

Determine the largest biopsy size from the histology report

HistolDx

Extracts histological diagnosis

HistolExtrapolDx

Extract specific diagnoses from the histology report

HistolHistol

Extract the histology data from the report by removing negative findings

HistolMacDescrip

Cleans spelt numbers in histology report

HistolNumbOfBx

Extract the number of biopsies taken from histology report

HowManyTests

Number of tests done per month and year by indication

ListLookup

Extract from report, using words from a list

MetricByEndoscopist

Plot a metric by endoscopist

Myendo

Fake Endoscopies

Mypath

Fake Pathology report

NegativeRemove

Removes negative and normal sentences

NumberPerformed

Determine overall number of procedures performed

PathDataFrameFinalColon

Fake Lower GI Pathology Set

PathDataFrameFinal

Fake Upper GI Pathology Set

PatientFlow_CircosPlots

Create a Circos plot for patient flow

PolypLocator

Determine polyp location

SurveilCapacity

Number of tests done per month

SurveilFirstTest

Extracts the first test only per patient

SurveilLastTest

Extract the last test done by a patient only

SurveilLastToNow

Extract the last test done by a patient in days and how long ago

SurveilTimeByRow

Extract the time difference between each test in days

SurveySankey

Create a Sankey plot for patient flow

TermStandardLocation

Standardise location of biopsies or tissue samples

TheOGDReportFinal

Fake Upper GI Endoscopy Set