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 |