# ==================================================================== #
# TITLE:                                                               #
# AMR: An R Package for Working with Antimicrobial Resistance Data     #
#                                                                      #
# SOURCE CODE:                                                         #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# PLEASE CITE THIS SOFTWARE AS:                                        #
# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
# Journal of Statistical Software, 104(3), 1-31.                       #
# https://doi.org/10.18637/jss.v104.i03                                #
#                                                                      #
# Developed at the University of Groningen and the University Medical  #
# Center Groningen in the Netherlands, in collaboration with many      #
# colleagues from around the world, see our website.                   # 
#                                                                      #
# 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://amr-for-r.org              #
# ==================================================================== #

title: "AMR (for R)"
url: "https://amr-for-r.org/"

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    navbar-padding-y: "0.5rem"

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 GPL 2.0</a>. 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, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.'
    logo: '<a target="_blank" href="https://www.rug.nl"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a>'

home:
  sidebar:
    structure: [toc, authors]

navbar:
  title: "AMR (for R)"
  left:
    - text: "How to"
      icon: "fa-question-circle"
      menu:
      - text: "Conduct AMR Analysis"
        icon: "fa-directions"
        href: "articles/AMR.html"
      - text: "Generate Antibiogram (Trad./Syndromic/WISCA)"
        icon: "fa-file-prescription"
        href: "reference/antibiogram.html" # reference instead of an article
      - text: "Use AMR for Predictive Modelling (tidymodels)"
        icon: "fa-square-root-variable"
        href: "articles/AMR_with_tidymodels.html"
      - text: "Download Data Sets for Own Use"
        icon: "fa-database"
        href: "articles/datasets.html"
      - text: "Set User- Or Team-specific Package Settings"
        icon: "fa-gear"
        href: "reference/AMR-options.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: "reference/mdro.html"
      - text: "Work with WHONET Data"
        icon: "fa-globe-americas"
        href: "articles/WHONET.html"
      - text: "Apply EUCAST Rules"
        icon: "fa-exchange-alt"
        href: "articles/EUCAST.html"
      - text: "Get Taxonomy of a Microorganism"
        icon: "fa-bug"
        href: "reference/mo_property.html" # reference instead of an article
      - text: "Get Properties of an Antibiotic Drug"
        icon: "fa-capsules"
        href: "reference/ab_property.html" # reference instead of an article
      - text: "Get Properties of an Antiviral Drug"
        icon: "fa-capsules"
        href: "reference/av_property.html" # reference instead of an article
    - text: "AMR for Python"
      icon: "fab fa-python"
      href: "articles/AMR_for_Python.html"
    - text: "Manual"
      icon: "fa-book-open"
      href: "reference/index.html"
    - text: "Authors"
      icon: "fa-users"
      href: "authors.html"
  structure:
    right: [search, amrchangelog, amrgit]
  components:
    amrchangelog:
      text: "Changelog"
      icon: "fa-newspaper"
      href: "news/index.html"
    amrgit:
      text: "Source Code"
      icon: "fa-github"
      href: "https://github.com/msberends/AMR"

reference:
  - title: "Getting started"
    desc: >
      An overview of the package, its options for users and teams, and its 28 supported languages.
    contents:
    - "`AMR`"
    - "`AMR-options`"
    - "`translate`"
    - "`amr_course`"

  - title: "Cleaning data"
    desc: >
      Transform raw input of any kind into valid microorganisms with `as.mo()`, antimicrobials with `as.ab()`, and MIC values and disk diffusion zones with `as.mic()` and `as.disk()`, and retrieve their properties.
  - subtitle: "Microorganisms"
    contents:
    - "`as.mo`"
    - "`mo_property`"
    - "`mo_source`"
    - "`add_custom_microorganisms`"
    - "`mo_matching_score`"
  - subtitle: "Antimicrobials"
    contents:
    - "`as.ab`"
    - "`ab_property`"
    - "`ab_from_text`"
    - "`add_custom_antimicrobials`"
    - "`atc_online_property`"
  - subtitle: "Antivirals"
    contents:
    - "`as.av`"
    - "`av_property`"
    - "`av_from_text`"
  - subtitle: "Test results"
    contents:
    - "`as.mic`"
    - "`as.disk`"

  - title: "Interpreting results as SIR"
    desc: >
      Interpret MIC values and disk diffusion zones as SIR with `as.sir()`, according to EUCAST or CLSI, for every guideline year from 2011 to 2026, and apply interpretive rules. `as.sir()` also cleans existing SIR data.
    contents:
    - "`as.sir`"
    - "`interpretive_rules`"
    - "`custom_interpretive_rules`"

  - title: "Analysing data"
    desc: >
      Select first isolates with `first_isolate()`, generate traditional, combination, syndromic, and WISCA antibiograms with `antibiogram()` and `wisca()`, calculate resistance, and determine multidrug-resistant organisms.
  - subtitle: "Selecting isolates and antimicrobials"
    contents:
    - "`first_isolate`"
    - "`get_episode`"
    - "`key_antimicrobials`"
    - "`top_n_microorganisms`"
    - "`antimicrobial_selectors`"
    - "`guess_ab_col`"
    - "`availability`"
  - subtitle: "Generating antibiograms and WISCA"
    contents:
    - "`antibiogram`"
  - subtitle: "Calculating resistance and susceptibility"
    contents:
    - "`proportion`"
    - "`count`"
    - "`sir_combine`"
    - "`bug_drug_combinations`"
  - subtitle: "Determining multidrug resistance"
    contents:
    - "`mdro`"
    - "`custom_mdro_guideline`"

  - title: "Visualising data"
    desc: >
      Plot MIC values, disk zones, and SIR results in base R or `ggplot2`, with scales and colours tailored to AMR data.
    contents:
    - "`plot`"
    - "`ggplot_sir`"
    - "`ggplot_pca`"

  - title: "Modelling"
    desc: >
      Use AMR data types in `tidymodels` pipelines, and perform principal component analysis or distance calculations on resistance profiles.
    contents:
    - "`amr-tidymodels`"
    - "`pca`"
    - "`mean_amr_distance`"

  - title: "Reference data"
    desc: >
      The data sets underlying this package, all of which can also be [downloaded in other formats](../articles/datasets.html).
  - subtitle: "Microorganisms"
    contents:
    - "`microorganisms`"
    - "`microorganisms.codes`"
    - "`microorganisms.groups`"
  - subtitle: "Antimicrobials"
    contents:
    - "`antimicrobials`"
    - "`WHOCC`"
    - "`dosage`"
  - subtitle: "Breakpoints and intrinsic resistance"
    contents:
    - "`clinical_breakpoints`"
    - "`intrinsic_resistant`"
  - subtitle: "Example data"
    contents:
    - "`example_isolates`"
    - "`example_isolates_unclean`"
    - "`esbl_isolates`"
    - "`WHONET`"

  - title: "Utilities"
    desc: >
      Helper functions for pattern matching with `%like%`, ages, joining and italicising taxonomy, generating random test results, and data export.
    contents:
    - "`like`"
    - "`age`"
    - "`age_groups`"
    - "`join`"
    - "`italicise_taxonomy`"
    - "`random`"
    - "`export_ncbi_biosample`"
  - subtitle: "Statistical tests"
    contents:
    - "`g.test`"
    - "`kurtosis`"
    - "`skewness`"

  - title: "Deprecated functions"
    desc: >
      These still work, but show a warning and will be removed in a future version.
    contents:
    - "`AMR-deprecated`"
    - "`resistance_predict`"