# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Analysis                              #
#                                                                      #
# SOURCE                                                               #
# https://gitlab.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
#                                                                      #
# This R package is free software; you can freely use and distribute   #
# it for both personal and commercial purposes under the terms of the  #
# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
# the Free Software Foundation.                                        #
#                                                                      #
# This R package was created for academic research and was publicly    #
# released in the hope that it will be useful, but it comes WITHOUT    #
# ANY WARRANTY OR LIABILITY.                                           #
# Visit our website for more info: https://msberends.gitab.io/AMR.     #
# ==================================================================== #

url: https://msberends.gitlab.io/AMR

title: 'AMR (for R)'

navbar:
  title: 'AMR (for R)'
  left:
    - text: 'Home'
      icon: 'fa-home'
      href: 'index.html'
    - text: 'How to'
      icon: 'fa-question-circle'
      menu:
      - text: 'Conduct AMR analysis'
        icon: 'fa-directions'
        href: 'articles/AMR.html'
      - text: 'Predict antimicrobial resistance'
        icon: 'fa-dice'
        href: 'articles/Predict.html'
      - text: 'Apply EUCAST rules'
        icon: 'fa-exchange-alt'
        href: 'articles/EUCAST.html'
      - text: 'Get properties of a microorganism'
        icon: 'fa-bug'
        href: 'articles/mo_property.html'
      - text: 'Get properties of an antibiotic'
        icon: 'fa-capsules'
        href: 'articles/ab_property.html'
      - text: 'Create frequency tables'
        icon: 'fa-sort-amount-down'
        href: 'articles/freq.html'
      - text: 'Use the G-test'
        icon: 'fa-clipboard-check'
        href: 'articles/G_test.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/'
  right:
    - text: 'Source Code'
      icon: 'fab fa-gitlab'
      href: 'https://gitlab.com/msberends/AMR'
    - 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](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
  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 # use logos in this folder
  params:
    noindex: false
    bootswatch: flatly
    docsearch:
      # using algolia.com
      api_key: 'f737050abfd4d726c63938e18f8c496e'
      index_name: 'amr'
