# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Analysis                              #
#                                                                      #
# AUTHORS                                                              #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)           #
#                                                                      #
# LICENCE                                                              #
# This package is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0,    #
# as published by the Free Software Foundation.                        #
#                                                                      #
# This R package is distributed in the hope that it will be useful,    #
# but WITHOUT ANY WARRANTY; without even the implied warranty of       #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the        #
# GNU General Public License version 2.0 for more details.             #
# ==================================================================== #

url: https://msberends.gitlab.io

title: 'AMR (for R)'

navbar:
  title: 'AMR (for R)'
  left:
    - text: 'Home'
      icon: 'fa-home'
      href: 'index.html'
    - text: 'Get Started'
      icon: 'fa-directions'
      href: 'articles/AMR.html'
    - text: 'Manual'
      icon: 'fa-book-open'
      href: 'reference/'
    - text: 'Authors'
      icon: 'fa-users'
      href: 'authors.html'
    - text: 'Changelog'
      icon: 'far fa-newspaper'
      href: 'news/'
    - text: 'Source Code'
      icon: 'fab fa-gitlab'
      href: 'https://gitlab.com/msberends/AMR'
  right:
    - text: 'Licence'
      icon: 'fa-book'
      href: 'LICENSE-text.html'

reference:
- title: Cleaning your data
  desc: >
    Functions for cleaning and optimising your data, to be able
    to add variables later on (like taxonomic properties) or to
    fix and extend antibiotic interpretations by applying EUCAST rules.
  contents:
  - starts_with("as.")
  - '`eucast_rules`'
  - '`read.4D`'
- title: Adding variables to your data
  desc: >
    Functions to add new data to existing data, like the determination
    of first isolates,
  contents:
  - '`first_isolate`'
  - '`mdro`'
  - '`key_antibiotics`'
  - '`mo_property`'
  - '`ab_property`'
  - '`atc_property`'
  - '`abname`'
  - '`age`'
  - '`age_groups`'
  - '`p.symbol`'
  - '`join`'
- title: Analysing your data
  desc: >
    Functions for conducting AMR analysis
  contents:
  - '`count`'
  - '`portion`'
  - '`freq`'
  - '`g.test`'
  - '`ggplot_rsi`'
  - '`kurtosis`'
  - '`resistance_predict`'
  - '`rsi`'
  - '`skewness`'
- title: Included data sets
  desc: >
    References for microorganisms and antibiotics, and even a
    genuine data set with isolates from septic patients.
  contents:
  - '`antibiotics`'
  - '`microorganisms`'
  - '`septic_patients`'
  - '`microorganisms.certe`'
  - '`microorganisms.old`'
  - '`microorganisms.umcg`'
  - '`supplementary_data`'
- title: Other
  desc: ~
  contents:
  - '`get_locale`'
  - '`like`'
  - '`mo_failures`'
  - '`mo_renamed`'

authors:
  Matthijs S. Berends:
    href: https://www.rug.nl/staff/m.s.berends/
  Christian F. Luz:
    href: https://www.rug.nl/staff/c.f.luz/
  Corinna Glasner:
    href: https://www.rug.nl/staff/c.glasner/
  Alex W. Friedrich:
    href: https://www.rug.nl/staff/a.w.friedrich/
  Bhanu N. M. Sinha:
    href: https://www.rug.nl/staff/b.sinha/

template:
  assets: pkgdown/logos
  params:
    noindex: false
    bootswatch: flatly
    docsearch:
      # using algolia.com
      api_key: 'f737050abfd4d726c63938e18f8c496e'
      index_name: 'amr'
