# ==================================================================== #
# 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.gitlab.io/AMR.    #
# ==================================================================== #

title: 'AMR (for R)'
url: 'https://msberends.gitlab.io/AMR'
development:
  mode: release # improves indexing by search engines
news:
  one_page: true

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/resistance_predict.html'
      - text: 'Determine multi-drug resistance (MDR)'
        icon: 'fa-skull-crossbones'
        href: 'articles/MDR.html'
      - text: 'Work with WHONET data'
        icon: 'fa-globe-americas'
        href: 'articles/WHONET.html'
      - text: 'Import data from SPSS/SAS/Stata'
        icon: 'fa-file-upload'
        href: 'articles/SPSS.html'
      - text: 'Apply EUCAST rules'
        icon: 'fa-exchange-alt'
        href: 'articles/EUCAST.html'
      - text: 'Get properties of a microorganism'
        icon: 'fa-bug'
        href: 'reference/mo_property.html' # reference instead of article
      - text: 'Get properties of an antibiotic'
        icon: 'fa-capsules'
        href: 'reference/ab_property.html' # reference instead of article
      - text: 'Create frequency tables'
        icon: 'fa-sort-amount-down'
        href: 'articles/freq.html'
      - text: 'Use the G-test'
        icon: 'fa-clipboard-check'
        href: 'reference/g.test.html' # reference instead of article
      - text: 'Other: benchmarks'
        icon: 'fa-shipping-fast'
        href: 'articles/benchmarks.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: 'Background information'
    desc: >
      Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
      for more information about how to work with functions in this package.
    contents:
    - '`AMR`'
    - '`catalogue_of_life`'
    - '`catalogue_of_life_version`'
    - '`WHOCC`'
  - 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.")
    - '`mo_source`'
    - '`eucast_rules`'
    - '`rsi_translation`'
    - '`guess_ab_col`'
    - '`read.4D`'
  - title: 'Adding variables to your data'
    desc: >
      Functions to add new data to existing data, like the determination
      of first isolates, multi-drug resistant microorganisms (MDRO), getting
      properties of microorganisms or antibiotics and determining the age of
      patients or divide ages into age groups.
    contents:
    - '`first_isolate`'
    - '`mdro`'
    - '`key_antibiotics`'
    - '`mo_property`'
    - '`ab_property`'
    - '`age`'
    - '`age_groups`'
    - '`p.symbol`'
    - '`join`'
    - '`atc_online_property`'
  - title: 'Analysing your data'
    desc: >
      Functions for conducting AMR analysis, like counting isolates, calculating
      resistance or susceptibility, creating frequency tables or make plots.
    contents:
    - '`availability`'
    - '`count`'
    - '`portion`'
    - '`filter_ab_class`'
    - '`freq`'
    - '`g.test`'
    - '`ggplot_rsi`'
    - '`kurtosis`'
    - '`resistance_predict`'
    - '`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`'
    - '`WHONET`'
    - '`microorganisms.codes`'
    - '`microorganisms.old`'
  - title: Other functions
    desc: >
      These functions are mostly for internal use, but some of
      them may also be suitable for your analysis. Especially the
      'like' function can be useful: `if (x %like% y) {...}`.
    contents:
    - '`get_locale`'
    - '`like`'
  - title: Deprecated functions
    desc: >
      These functions are deprecated, meaning that they still
      work but show a warning with every use and will be removed
      in a future version.
    contents:
    - '`AMR-deprecated`'

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'