# ==================================================================== #
# TITLE                                                                #
# AMR: An R Package for Working with Antimicrobial Resistance Data     #
#                                                                      #
# SOURCE                                                               #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# CITE AS                                                              #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C    #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance  #
# Data. Journal of Statistical Software, 104(3), 1-31.                 #
# doi:10.18637/jss.v104.i03                                            #
#                                                                      #
# Developed at the University of Groningen, the Netherlands, in        #
# collaboration with non-profit organisations Certe Medical            #
# Diagnostics & Advice, and University Medical Center Groningen.       # 
#                                                                      #
# 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.                                        #
# We created this package for both routine data analysis and academic  #
# research and it was publicly released in the hope that it will be    #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
#                                                                      #
# Visit our website for the full manual and a complete tutorial about  #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
# ==================================================================== #

title: "AMR (for R)"
url: "https://msberends.github.io/AMR/"

template:
  bootstrap: 5
  bootswatch: "flatly"
  assets: "pkgdown/logos" # use logos in this folder
  bslib:
    code_font: {google: "Fira Code"}
    # body-text-align: "justify"
    line-height-base: 1.75
    # the green "success" colour of this bootstrap theme should be the same as the green in our logo
    success: "#128f76"
    link-color: "#128f76"
    navbar-padding-y: "0.5rem"
  opengraph:
    twitter:
      creator: "@msberends"
      card: summary_large_image

news:
  one_page: true
  cran_dates: true

footer:
  structure:
    left: [devtext]
    right: [logo]
  components:
    devtext: '<code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl">University Medical Center Groningen</a> in The Netherlands.'
    logo: '<a target="_blank" href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a>'

home:
  sidebar:
    structure: [toc, links, authors]

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: "Data sets for download / own use"
        icon: "fa-database"
        href: "articles/datasets.html"
      - text: "Conduct principal component analysis for AMR"
        icon: "fa-compress"
        href: "articles/PCA.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 an article
      - text: "Get properties of an antibiotic"
        icon: "fa-capsules"
        href: "reference/ab_property.html" # reference instead of an article
      - text: "Get properties of an antiviral agent"
        icon: "fa-capsules"
        href: "reference/av_property.html" # reference instead of an article
    - text: "Manual"
      icon: "fa-book-open"
      href: "reference/index.html"
    - text: "Authors"
      icon: "fa-users"
      href: "authors.html"
    - text: "Changelog"
      icon: "far fa-newspaper"
      href: "news/index.html"
  right:
    - text: "Source Code"
      icon: "fab fa-github"
      href: "https://github.com/msberends/AMR"
    # - text: "Survey"
    #   icon: "fa-clipboard-list"
    #   href: "survey.html"

reference:
  - title: "Preparing data: microorganisms"
    desc: >
      These functions are meant to get taxonomically valid properties of microorganisms from any input.
      Use `mo_source()` to teach this package how to translate your own codes to valid microorganism codes.
    contents:
    - "`as.mo`"
    - "`mo_property`"
    - "`mo_source`"

  - title: "Preparing data: antibiotics"
    desc: >
      Use these functions to get valid properties of antibiotics from any input or to clean your input.
      You can even retrieve drug names and doses from clinical text records, using `ab_from_text()`.
    contents:
    - "`as.ab`"
    - "`ab_property`"
    - "`ab_from_text`"
    - "`atc_online_property`"
    - "`add_custom_antimicrobials`"

  - title: "Preparing data: antimicrobial resistance"
    desc: >
      With `as.mic()` and `as.disk()` you can transform your raw input to valid MIC or disk diffusion values.
      Use `as.rsi()` for cleaning raw data to let it only contain "R", "I" and "S", or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines.
      Afterwards, you can extend antibiotic interpretations by applying [EUCAST rules](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) with `eucast_rules()`.
    contents:
    - "`as.rsi`"
    - "`as.mic`"
    - "`as.disk`"
    - "`eucast_rules`"
    - "`custom_eucast_rules`"

  - title: "Analysing data: antimicrobial resistance"
    desc: >
      Use these function for the analysis part. You can use `susceptibility()` or `resistance()` on any antibiotic column.
      Be sure to first select the isolates that are appropiate for analysis, by using `first_isolate()` or `is_new_episode()`.
      You can also filter your data on certain resistance in certain antibiotic classes (`carbapenems()`, `aminoglycosides()`), or determine multi-drug resistant microorganisms (MDRO, `mdro()`).
    contents:
    - "`proportion`"
    - "`count`"
    - "`is_new_episode`"
    - "`first_isolate`"
    - "`key_antimicrobials`"
    - "`mdro`"
    - "`count`"
    - "`plot`"
    - "`ggplot_rsi`"
    - "`bug_drug_combinations`"
    - "`antibiotic_class_selectors`"
    - "`mean_amr_distance`"
    - "`resistance_predict`"
    - "`guess_ab_col`"
    
  - title: "Other: antiviral drugs"
    desc: >
      This package also provides extensive support for antiviral agents, even though it is not the primary
      scope of this package. Working with data containing information about antiviral drugs was never easier.
      Use these functions to get valid properties of antiviral drugs from any input or to clean your input.
      You can even retrieve drug names and doses from clinical text records, using `av_from_text()`.
    contents:
    - "`as.av`"
    - "`av_property`"
    - "`av_from_text`"

  - title: "Other: background information on included data"
    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`"
    - "`example_isolates`"
    - "`microorganisms`"
    - "`microorganisms.codes`"
    - "`antibiotics`"
    - "`intrinsic_resistant`"
    - "`dosage`"
    - "`WHOCC`"
    - "`example_isolates_unclean`"
    - "`rsi_translation`"
    - "`WHONET`"

  - title: "Other: miscellaneous 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:
    - "`age_groups`"
    - "`age`"
    - "`availability`"
    - "`get_AMR_locale`"
    - "`ggplot_pca`"
    - "`italicise_taxonomy`"
    - "`join`"
    - "`like`"
    - "`mo_matching_score`"
    - "`pca`"
    - "`random`"

  - title: "Other: statistical tests"
    desc: >
      Some statistical tests or methods are not part of base R and were added to this package for convenience.
    contents:
    - "`g.test`"
    - "`kurtosis`"
    - "`skewness`"

  - title: "Other: deprecated functions"
    desc: >
      These functions are deprecated, meaning that they will still
      work but show a warning with every use and will be removed
      in a future version.
    contents:
    - "`AMR-deprecated`"