Man pages for ropensci/EndoMineR
Functions to mine endoscopic and associated pathology datasets

BarrettsAllFollow up group determination
BarrettsBasicNumbersBarretts Basic Numbers
BarrettsBxQualBarrett's number of biopsies
Barretts_CRIMCRIM status Barrett's
BarrettsDDRQualDysplasia detection rate on surveillance
BarrettsDocumentQualAnalysis of Barrett's Documentation Quality
BarrettsEMRGradesNumber of Barrett's EMRs by grade
Barretts_EventTypeTherapeutic subtypes
Barretts_FUTypeFollow up group determination
BarrettsParisEMRParis vs histopath Barrett's
BarrettsPathDetectQualDysplasia detection on surveillance
Barretts_PathStageWorst pathological stage Barrett's
Barretts_PragueScorePrague score extraction
BarrettssRFACathRFA catheter use
BarrettsSurveilHow many Barrett's patients had surveillance
BarrettsSurveil_HospNumUnique Hospital Numbers of Barrett's patients
ColonFinalFake Lower GI Endoscopy Set
ColumnCleanUpTidies up messy columns
ColumnCleanUpAllTidies up all columns
EndoMineREndoMineR: A package for analysis of endoscopic and related...
EndoscAllExtracts the columns from the raw report
EndoscEndoscopistCleans endoscopist column if present
EndoscFindingsCleans Procedure performed column if present
EndoscIndicationsCleans indications column if present
EndoscInstrumentCleans instrument column if present
EndoscMedsCleans medication column if present
EndoscProcPerformedCleans Procedure performed column if present
ExtractorExtracts the columns from the raw report
GRS_Type_Assess_By_UnitCreate GRS metrics by endoscopist (X-ref with pathology)
HistolAccessionNumberExtract histological accession number
HistolAllClean up all Histology data
HistolBxSizeDetermine the largest biopsy size from the histology report
HistolDxExtracts histological diagnosis
HistolExtrapolDxExtract specific diagnoses from the histology report
HistolHistolExtract the histology data from the report by removing...
HistolMacDescripCleans spelt numbers in histology report
HistolNumbOfBxExtract the number of biopsies taken from histology report
HowManyTestsNumber of tests done per month and year by indication
ListLookupExtract from report, using words from a list
MetricByEndoscopistPlot a metric by endoscopist
MyendoFake Endoscopies
MypathFake Pathology report
NegativeRemoveRemoves negative and normal sentences
NumberPerformedDetermine overall number of procedures performed
PathDataFrameFinalFake Upper GI Pathology Set
PathDataFrameFinalColonFake Lower GI Pathology Set
PatientFlow_CircosPlotsCreate a Circos plot for patient flow
PolypLocatorDetermine polyp location
SurveilCapacityNumber of tests done per month
SurveilFirstTestExtracts the first test only per patient
SurveilLastTestExtract the last test done by a patient only
SurveilLastToNowExtract the last test done by a patient in days and how long...
SurveilTimeByRowExtract the time difference between each test in days
SurveySankeyCreate a Sankey plot for patient flow
TermStandardLocationStandardise location of biopsies or tissue samples
TheOGDReportFinalFake Upper GI Endoscopy Set
ropensci/EndoMineR documentation built on Sept. 29, 2018, 5:32 a.m.