All functions
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BarrettsAll
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Follow up group determination |
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BarrettsBasicNumbers
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Barretts Basic Numbers |
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BarrettsBxQual
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Barrett's number of biopsies |
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Barretts_CRIM
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CRIM status Barrett's |
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BarrettsDDRQual
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Dysplasia detection rate on surveillance |
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BarrettsDocumentQual
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Analysis of Barrett's Documentation Quality |
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BarrettsEMRGrades
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Number of Barrett's EMRs by grade |
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Barretts_EventType
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Therapeutic subtypes |
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Barretts_FUType
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Follow up group determination |
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BarrettsParisEMR
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Paris vs histopath Barrett's |
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BarrettsPathDetectQual
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Dysplasia detection on surveillance |
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Barretts_PathStage
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Worst pathological stage Barrett's |
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Barretts_PragueScore
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Prague score extraction |
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BarrettssRFACath
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RFA catheter use |
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BarrettsSurveil_HospNum
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Unique Hospital Numbers of Barrett's patients |
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BarrettsSurveil
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How many Barrett's patients had surveillance |
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ColonFinal
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Fake Lower GI Endoscopy Set |
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ColumnCleanUpAll
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Tidies up all columns |
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ColumnCleanUp
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Tidies up messy columns |
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Endomerge2
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Endomerge |
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EndoMineR
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EndoMineR: A package for analysis of endoscopic and related pathology |
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EndoscAll
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Extracts the columns from the raw report |
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EndoscEndoscopist
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Cleans endoscopist column if present |
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EndoscFindings
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Cleans Procedure performed column if present |
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EndoscIndications
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Cleans indications column if present |
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EndoscInstrument
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Cleans instrument column if present |
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EndoscMeds
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Cleans medication column if present |
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EndoscProcPerformed
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Cleans Procedure performed column if present |
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Extractor
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Extracts the columns from the raw report |
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GRS_Type_Assess_By_Unit
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Create GRS metrics by endoscopist (X-ref with pathology) |
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HistolAccessionNumber
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Extract histological accession number |
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HistolAll
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Clean up all Histology data |
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HistolBxSize
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Determine the largest biopsy size from the histology report |
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HistolDx
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Extracts histological diagnosis |
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HistolExtrapolDx
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Extract specific diagnoses from the histology report |
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HistolHistol
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Extract the histology data from the report by removing negative findings |
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HistolMacDescrip
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Cleans spelt numbers in histology report |
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HistolNumbOfBx
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Extract the number of biopsies taken from histology report |
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HowManyTests
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Number of tests done per month and year by indication |
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ListLookup
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Extract from report, using words from a list |
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MetricByEndoscopist
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Plot a metric by endoscopist |
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Myendo
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Fake Endoscopies |
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Mypath
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Fake Pathology report |
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NegativeRemove
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Removes negative and normal sentences |
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NumberPerformed
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Determine overall number of procedures performed |
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PathDataFrameFinalColon
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Fake Lower GI Pathology Set |
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PathDataFrameFinal
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Fake Upper GI Pathology Set |
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PatientFlow_CircosPlots
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Create a Circos plot for patient flow |
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PolypLocator
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Determine polyp location |
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SurveilCapacity
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Number of tests done per month |
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SurveilFirstTest
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Extracts the first test only per patient |
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SurveilLastTest
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Extract the last test done by a patient only |
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SurveilLastToNow
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Extract the last test done by a patient in days and how long ago |
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SurveilTimeByRow
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Extract the time difference between each test in days |
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SurveySankey
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Create a Sankey plot for patient flow |
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TermStandardLocation
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Standardise location of biopsies or tissue samples |
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TheOGDReportFinal
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Fake Upper GI Endoscopy Set |