_pkgdown.yaml

template:
  params:
    bootswatch: paper
    
navbar:
  type: inverse
  left:
    - text: "Home"
      href: index.html
    - text: "News"
      href: news/index.html
    - text: "Tutorials"
      menu:
        - text: "EndoMineR Principles"
          href: articles/EndoMineRPrinciples.html
        - text: "Package overview"
          href: articles/EndoMineR.html
        - text: "Analysis"
          href: articles/Analysis.html
        - text: "Barrett's"
          href: articles/Barretts.html
        - text: "Lower GI Polyps"
          href: articles/Polyps.html
        - text: "Data"
          href: articles/Data.html
    - text: "Functions"
      href: reference/index.html
  right:
    - icon: fa fa-bullseye
      href: http://gastrodatascience.com
    - icon: fa fa-twitter
      href: https://twitter.com/GastroDS
    - icon: fa-github fa-lg
      href: https://github.com/ropensci/EndoMineR
    - icon: far fa-book
      href: http://www.gastroenterologybook.com/
    - icon:  fas fa-stethoscope
      href: https://www.nhs.uk/profiles/consultant/6029157
reference:
  - title: "NLP - Text Cleaning and Extraction:"
    desc: "Functions to clean raw text"
    contents:
      - textPrep
      - Extractor
      - DictionaryInPlaceReplace
      - NegativeRemove
      - NegativeRemoveWrapper
      - spellCheck
      - ColumnCleanUp
      - ListLookup
  - title: "NLP - Text merging:"
    desc: "Functions to help merge datasets"
    contents:
      - EndoPaste
      - Endomerge2
  - title: "NLP - Lexicons:"
    desc: "Basic lexicons"
    contents:
      - HistolType
      - LocationList
      - LocationListUpper
      - LocationListUniversal
      - LocationListLower
      - RFACath
      - EventList
      - BiopsyIndex
      - GISymptomsList
      - WordsToNumbers
  - title: "Basic Column mutators"
    desc: "Basic Column mutators"
    contents:
      - ExtrapolatefromDictionary
      - ListLookup
      - EntityPairs_OneSentence
      - EntityPairs_TwoSentence
      - MyImgLibrary
  - title: "Specific Text Cleaning - Endoscopy specific cleaning functions:"
    desc: "Functions to help clean endoscopy reports"
    contents:
      - EndoscEndoscopist
      - EndoscInstrument
      - EndoscMeds
      - EndoscopyEvent
  - title: "Specific Text Cleaning - Histology specific cleaning functions:"
    desc: "Functions to help clean histology text"
    contents:
      - HistolNumbOfBx
      - HistolBxSize
      - HistolTypeAndSite
  - title: "Basic Analysis Helper - Grouping by endoscopist"
    desc: "Grouping by endoscopist"
    contents:
      - MetricByEndoscopist
      - CategoricalByEndoscopist
  - title: "Basic Analysis - Surveillance Functions:"
    desc: "Functions to analyse surveillance intervals"
    contents:
      - SurveilTimeByRow
      - SurveilLastTest
      - SurveilFirstTest
      - TimeToStatus
      - HowManyOverTime
  - title: "Disease Specific Analysis - Barretts Data"
    desc: "Functions for reading and writing Barretts Data."
    contents:
      - starts_with("Barretts")
  - title: "Disease Specific Analysis - Polyp functions:"
    desc: "Polyp analysis"
    contents:
      - GRS_Type_Assess_By_Unit
  - title: "Patient Flow functions:"
    desc: "Visualise patient flow"
    contents:
      - SurveySankey
      - PatientFlow_CircosPlots
      - PatientFlowIndividual
  - title: "Data overview:"
    desc: "Basic consort diagrams"
    contents:
      - sanity
  - title: "Data Presentation helpers:"
    desc: "Functions to help with data visualisation"
    contents:
      - theme_Publication
      - scale_fill_Publication
      - scale_colour_Publication
      - EndoBasicGraph
  - title: internal
    desc: "undocumented functions"
    contents:
      - ColonFinal
      - EndoMineR
      - Eosinophilics
      - IBD_Scores
      - Myendo
      - Mypath
      - PathDataFrameFinal
      - PathDataFrameFinalColon
      - TheOGDReportFinal
      - dev_ExtrapolateOPCS4Prep
      - vColon