Files in ropensci/EndoMineR

Functions to mine endoscopic and associated pathology datasets

.Rbuildignore

.gitattributes

.github/CONTRIBUTING.md

.github/FUNDING.yml

.gitignore

.travis.yml

CONTRIBUTING.md

DESCRIPTION

EndoMineR_devSite.Rproj

LICENSE

Meta/vignette.rds

NAMESPACE

NEWS.md R/Basic_CleanUp.R R/Basic_EndoPathExtractors.R R/EndoFakeData.R R/EndoMineR.R R/EndoMineR1.R R/Graphics.R R/Lexicons.R R/Module_Barretts.R R/Module_Eosinophil.R R/Module_IBD.R R/Module_Polyps.R R/ReportBuilder.R R/data.R README.Rmd README.md

_pkgdown.yaml

codecov.yml

data-raw/EndoFakeData.R

data-raw/data/FindingsText

data-raw/data/FindingsTextColon.txt

data-raw/data/HistolClinDetText

data-raw/data/HistolDxText

data-raw/data/HistolMacDescription.txt

data-raw/data/HistolText

data-raw/data/HistolTextColon

data-raw/data/Histopath_ClinDetPhrasesColon.txt

data-raw/data/Histopath_DxRawColon.txt

data-raw/data/Histopath_MacDescripPhrasesColon.txt

data/ColonFinal.rda

data/Myendo.rda

data/Mypath.rda

data/PathDataFrameFinal.rda

data/PathDataFrameFinalColon.rda

data/TheOGDReportFinal.rda

data/vColon.rda

doc/Analysis.R doc/Analysis.Rmd

doc/Analysis.html

doc/Barretts.R doc/Barretts.Rmd

doc/Barretts.html

doc/Data.R doc/Data.Rmd

doc/Data.html

doc/EndoMineR.R doc/EndoMineR.Rmd

doc/EndoMineR.html

doc/Polyps.R doc/Polyps.Rmd

doc/Polyps.html

docs/404.html

docs/CONTRIBUTING.html

docs/articles/Analysis.R

docs/articles/Analysis.html

docs/articles/Analysis_files/figure-html/exampleEndoscChopperMeds-1.png

docs/articles/Analysis_files/figure-html/exampleHowManyTests-1.png

docs/articles/Barretts.R

docs/articles/Barretts.html

docs/articles/Barretts_files/figure-html/exampleBarrettsBasicNumbers-1.png

docs/articles/Barretts_files/figure-html/exampleBarrettsQuality_AnalysisBiopsyNumber-1.png

docs/articles/Barretts_files/figure-html/exampleBarrettsQuality_AnalysisDocumentation-1.png

docs/articles/Barretts_files/figure-html/exampleBarrettsSurveillance_PathDetection-1.png

docs/articles/Barretts_files/figure-html/exampleBarrettsTherapeuticsRFA_ByCatheter-1.png

docs/articles/Barretts_files/figure-html/exampleBarretts_LesionRecognitionEMR2-1.png

docs/articles/Data.R

docs/articles/Data.html

docs/articles/Data_files/figure-html/pressure-1.png

docs/articles/EndoMineR.R

docs/articles/EndoMineR.html

docs/articles/EndoMineRPrinciples.R

docs/articles/EndoMineRPrinciples.html

docs/articles/Polyps.html

docs/articles/Polyps_files/figure-html/exampleGRSGraph-1.png

docs/articles/img/BarrettsGuide.png

docs/articles/img/EndoMinR_Clean.png

docs/articles/img/EndoMineRBasic.jpg

docs/articles/img/EndoMineROverView.png

docs/articles/img/EndoMineRPrincip_Dataset.png

docs/articles/img/EndoMineRPrincip_DiagYield.png

docs/articles/img/EndoMineRPrincip_Summary.png

docs/articles/img/EndoMineRSurveillanceDataset.png

docs/articles/img/EndoMineR_Circos.svg

docs/articles/img/EndoMineR_EndoscopyClean.png

docs/articles/img/EndoMineR_Extractor.svg

docs/articles/img/EndoMineR_FunctionStructure.svg

docs/articles/img/EndoMineR_HistopExtrapol.png

docs/articles/img/EndoMineR_Sankey.svg

docs/articles/img/EndoMineR_Surveillance.svg

docs/articles/img/TypicalReportForGastroDSEndoMinerVignette.svg

docs/articles/index.html

docs/articles/style.css

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/extra.css

docs/index.html

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/BarrettsAll.html

docs/reference/BarrettsBasicNumbers-1.png

docs/reference/BarrettsBasicNumbers.html

docs/reference/BarrettsBxQual-1.png

docs/reference/BarrettsBxQual.html

docs/reference/BarrettsDDRQual.html

docs/reference/BarrettsDocumentQual-1.png

docs/reference/BarrettsDocumentQual.html

docs/reference/BarrettsEMRGrades-1.png

docs/reference/BarrettsEMRGrades.html

docs/reference/BarrettsParisEMR.html

docs/reference/BarrettsPathDetectQual-1.png

docs/reference/BarrettsPathDetectQual.html

docs/reference/BarrettsSurveil.html

docs/reference/BarrettsSurveil_HospNum.html

docs/reference/Barretts_CRIM.html

docs/reference/Barretts_EventType.html

docs/reference/Barretts_FUType.html

docs/reference/Barretts_PathStage.html

docs/reference/Barretts_PragueScore.html

docs/reference/BarrettssRFACath-1.png

docs/reference/BarrettssRFACath.html

docs/reference/BiopsyIndex.html

docs/reference/CategoricalByEndoscopist.html

docs/reference/ColonFinal.html

docs/reference/ColumnCleanUp.html

docs/reference/ColumnCleanUpAll.html

docs/reference/DictionaryInPlaceReplace.html

docs/reference/EbdoMineR.html

docs/reference/EndoBasicGraph-1.png

docs/reference/EndoBasicGraph.html

docs/reference/EndoMineR.html

docs/reference/EndoPaste.html

docs/reference/Endomerge2.html

docs/reference/EndoscAll.html

docs/reference/EndoscEndoscopist.html

docs/reference/EndoscFindings.html

docs/reference/EndoscIndications.html

docs/reference/EndoscInstrument.html

docs/reference/EndoscMeds.html

docs/reference/EndoscProcPerformed.html

docs/reference/Endoscopies.html

docs/reference/EndoscopyEvent.html

docs/reference/EntityPairs_OneSentence.html

docs/reference/EntityPairs_TwoSentence.html

docs/reference/EventList.html

docs/reference/Extractor.html

docs/reference/Extractor2.html

docs/reference/ExtrapolatefromDictionary.html

docs/reference/GISymptomsList.html

docs/reference/GRS_Type_Assess_By_Unit.html

docs/reference/HistolAccessionNumber.html

docs/reference/HistolAll.html

docs/reference/HistolBxSize.html

docs/reference/HistolDx.html

docs/reference/HistolExtrapolDx.html

docs/reference/HistolHistol.html

docs/reference/HistolMacDescrip.html

docs/reference/HistolNumbOfBx.html

docs/reference/HistolType.html

docs/reference/HistolTypeAndSite.html

docs/reference/Histop_df.html

docs/reference/HowManyOverTime.html

docs/reference/HowManyTests-1.png

docs/reference/HowManyTests.html

docs/reference/ListLookup.html

docs/reference/LocationList.html

docs/reference/LocationListLower.html

docs/reference/LocationListUniversal.html

docs/reference/LocationListUpper.html

docs/reference/MetricByEndoscopist-1.png

docs/reference/MetricByEndoscopist.html

docs/reference/MyImgLibrary.html

docs/reference/Myendo.html

docs/reference/Mypath.html

docs/reference/NegativeRemove.html

docs/reference/NegativeRemoveWrapper.html

docs/reference/NewLines.html

docs/reference/NumberPerformed.html

docs/reference/PathDataFrameFinal.html

docs/reference/PathDataFrameFinalColon.html

docs/reference/PatientFlow_CircosPlots-1.png

docs/reference/PatientFlow_CircosPlots-2.png

docs/reference/PatientFlow_CircosPlots-3.png

docs/reference/PatientFlow_CircosPlots.html

docs/reference/PolypLocator.html

docs/reference/RFACath.html

docs/reference/SurveilCapacity.html

docs/reference/SurveilFirstTest.html

docs/reference/SurveilLastTest.html

docs/reference/SurveilLastToNow.html

docs/reference/SurveilTimeByRow.html

docs/reference/SurveySankey.html

docs/reference/TermStandardLocation.html

docs/reference/TheOGDReportFinal.html

docs/reference/TimeToStatus.html

docs/reference/WordsToNumbers.html

docs/reference/dev_ExtrapolateOPCS4Prep.html

docs/reference/figures/BarrettsBasicNumbers.svg

docs/reference/figures/BarrettsEMR_By_Pathology.svg

docs/reference/figures/BarrettsRFA_CatheterType.svg

docs/reference/figures/Barretts_Shortfall.png

docs/reference/figures/EndoMinR_Clean.png

docs/reference/figures/EndoMineR_Barretts.svg

docs/reference/figures/EndoMineR_BarrettsClean.png

docs/reference/figures/EndoMineR_Circos.svg

docs/reference/figures/EndoMineR_EndoscopyClean.svg

docs/reference/figures/EndoMineR_Extractor.svg

docs/reference/figures/EndoMineR_FunctionStructure.svg

docs/reference/figures/EndoMineR_HistopExtrapol.svg

docs/reference/figures/EndoMineR_Sankey.svg

docs/reference/figures/EndoMineR_Surveillance.svg

docs/reference/figures/GradeBarretts.svg

docs/reference/figures/MetricByEndoscopist.png

docs/reference/figures/Rplot.png

docs/reference/figures/Rplot01.svg

docs/reference/figures/TypicalReportForGastroDSEndoMinerVignette.svg

docs/reference/index.html

docs/reference/sanity.html

docs/reference/scale_colour_Publication.html

docs/reference/scale_fill_Publication.html

docs/reference/spellCheck.html

docs/reference/textPrep.html

docs/reference/theme_Publication.html

docs/reference/vColon.html

man/BarrettsAll.Rd man/BarrettsBxQual.Rd man/BarrettsParisEMR.Rd man/Barretts_FUType.Rd man/Barretts_PathStage.Rd man/Barretts_PragueScore.Rd man/BiopsyIndex.Rd man/CategoricalByEndoscopist.Rd man/ColonFinal.Rd man/ColumnCleanUp.Rd man/DictionaryInPlaceReplace.Rd man/EndoBasicGraph.Rd man/EndoMineR.Rd man/EndoPaste.Rd man/Endomerge2.Rd man/EndoscEndoscopist.Rd man/EndoscInstrument.Rd man/EndoscMeds.Rd man/EndoscopyEvent.Rd man/EntityPairs_OneSentence.Rd man/EntityPairs_TwoSentence.Rd man/Eosinophilics.Rd man/EventList.Rd man/Extractor.Rd man/ExtrapolatefromDictionary.Rd man/GISymptomsList.Rd man/GRS_Type_Assess_By_Unit.Rd man/HistolBxSize.Rd man/HistolNumbOfBx.Rd man/HistolType.Rd man/HistolTypeAndSite.Rd man/HowManyOverTime.Rd man/IBD_Scores.Rd man/ListLookup.Rd man/LocationList.Rd man/LocationListLower.Rd man/LocationListUniversal.Rd man/LocationListUpper.Rd man/MetricByEndoscopist.Rd man/MyImgLibrary.Rd man/Myendo.Rd man/Mypath.Rd man/NegativeRemove.Rd man/NegativeRemoveWrapper.Rd man/PathDataFrameFinal.Rd man/PathDataFrameFinalColon.Rd man/PatientFlowIndividual.Rd man/PatientFlow_CircosPlots.Rd man/RFACath.Rd man/SurveilFirstTest.Rd man/SurveilLastTest.Rd man/SurveilTimeByRow.Rd man/SurveySankey.Rd man/TheOGDReportFinal.Rd man/TimeToStatus.Rd man/WordsToNumbers.Rd man/dev_ExtrapolateOPCS4Prep.Rd

man/figures/BarrettsBasicNumbers.svg

man/figures/BarrettsEMR_By_Pathology.svg

man/figures/BarrettsRFA_CatheterType.svg

man/figures/Barretts_Shortfall.png

man/figures/EndoMinR_Clean.png

man/figures/EndoMineR_Barretts.svg

man/figures/EndoMineR_BarrettsClean.png

man/figures/EndoMineR_Circos.svg

man/figures/EndoMineR_EndoscopyClean.svg

man/figures/EndoMineR_Extractor.svg

man/figures/EndoMineR_FunctionStructure.svg

man/figures/EndoMineR_HistopExtrapol.svg

man/figures/EndoMineR_Sankey.svg

man/figures/EndoMineR_Surveillance.svg

man/figures/GradeBarretts.svg

man/figures/MetricByEndoscopist.png

man/figures/Rplot.png

man/figures/Rplot01.svg

man/figures/TypicalReportForGastroDSEndoMinerVignette.svg

man/sanity.Rd man/scale_colour_Publication.Rd man/scale_fill_Publication.Rd man/spellCheck.Rd man/textPrep.Rd man/theme_Publication.Rd man/vColon.Rd

paper/paper.bib

paper/paper.html

paper/paper.md

pkgdown/extra.css

tests/testthat.R

tests/testthat/.Rapp.history

tests/testthat/test.R vignettes/Analysis.Rmd vignettes/Barretts.Rmd vignettes/Data.Rmd vignettes/EndoMineR.Rmd vignettes/Polyps.Rmd

vignettes/img/BarrettsGuide.png

vignettes/img/EndoMinR_Clean.png

vignettes/img/EndoMineRBasic.jpg

vignettes/img/EndoMineRLogo.png

vignettes/img/EndoMineR_Circos.svg

vignettes/img/EndoMineR_Sankey.svg

vignettes/img/EndoMineR_Surveillance.svg

vignettes/img/TypicalReportForGastroDSEndoMinerVignette.svg

vignettes/style.css

ropensci/EndoMineR documentation built on March 14, 2023, 3:58 a.m.