_pkgdown.yml

destination: docs
template:
  params:
    bootswatch: flatly
  opengraph:
    image:
      src: reference/figures/logo.png
      alt: "Ramses: R package for Antimicrobial Stewardship & Surveillance"
    twitter:
      creator: "@peterdutey"
      card: summary
title: RAMSES
url: https://ramses-antibiotics.web.app/
figures:
  fig.align: 'center'

footer:
  structure: 
    left:
    right: built_with
    
authors:
    sidebar:
      roles: [aut, ctb, cre, res, rth, cph]
    University College London:
      href: "https://www.ucl.ac.uk"
      html: "<img src='https://ramses-antibiotics.web.app/reference/figures/partner-logos/UCL.png' height=28>"

navbar:
  right:
    - text: "Source"
      icon: "fab fa-github fa-lg"
      href: https://github.com/ramses-antibiotics/ramses-package/
    - text: "PASS"
      icon: "fas fa-capsules fa-lg"
      href: https://pass-antibiotics.github.io/

home:
  description: >
    Ramses is an analytical software package enabling hospitals to
    monitor and query their use of antibiotics and the management of
    infections.
  links:
  - text: Visit project website
    href: https://pass-antibiotics.github.io/

reference:
- title: Ramses object model
  desc:  S4 classes and methods handling `Ramses` objects
  contents:
  - RamsesObject-class
  - Patient-class
  - Encounter-class
  - MedicationRequest-class
  - TherapyEpisode-class
  - longitudinal_table
  - parenteral_changes
  - starts_with("clinical_feature_")
  - collect
  - compute
  - therapy_timeline
- title: Transform and validate data
  desc:  Functions to enrich and validate data before loading into the warehouse.
  contents:
  - starts_with("map_")
  - compute_DDDs
  - get_ATC_name
  - starts_with("validate_inpatient")
  - validate_prescriptions
  - validate_administrations
  - validate_investigations
  - validate_microbiology
- title: Load & link data
  desc:  Load records into the warehouse and create secondary information.
  contents:
  - starts_with("load_inpatient")
  - load_medications
  - transitive_closure_control
- title: Simulated sets of electronic health records
  contents:
  - patients
  - inpatient_episodes
  - inpatient_wards
  - inpatient_diagnoses
  - drug_prescriptions
  - drug_administrations
  - inpatient_microbiology  
  - inpatient_investigations
- title: Reference datasets
  desc:  Metadata provided with `Ramses`
  contents:
  - antibiotic_icd_indications
  - ccs
  - ccsr
  - download_icd10cm
  - import_icd
  - starts_with("reference_")
- title: Database administration
  desc:  Functions to set up and manage the `Ramses` database
  contents:
  - connect_local_database
  - create_mock_database
  - starts_with("bridge_")
  - create_therapy_episodes
- title: Index
  desc:  All functions in alphabetical order
  contents:
  - matches(".*")