# ==================================================================== #
# 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
  version_tooltip: "Latest development version"

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: Extended functions
    desc: >
      These functions are extensions of functions in other packages.
    contents:
    - "`extended-functions`"
  - title:  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"
