AMR/_pkgdown.yml

# ==================================================================== #
# 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://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:
    base_font: {google: "Lato"}
    heading_font: {google: "Lato"}
    code_font: {google: "Fira Code"}
    # body-text-align: "justify"
    line-height-base: 1.75
    # make top bar a bit wider
    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 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/assets/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/assets/logo_umcg.svg" style="max-width: 150px;"></a>'

home:
  sidebar:
    structure: [gpthelp, toc, links, authors]
    components:
      gpthelp: 
        text: '<a target="_blank" href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT.svg" style="width: 80%;"></a>'

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: "Generate Antibiogram (Trad./Syndromic/WISCA)"
        icon: "fa-file-prescription"
        href: "reference/antibiogram.html" # reference instead of an article
      - text: "Predict Antimicrobial Resistance"
        icon: "fa-dice"
        href: "articles/resistance_predict.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: "articles/MDR.html"
      - text: "Work with WHONET Data"
        icon: "fa-globe-americas"
        href: "articles/WHONET.html"
      # - text: "Import Data From SPSS/Stata"
      #   icon: "fa-file-upload"
      #   href: "articles/SPSS.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"
  right:
    - text: "Changelog"
      icon: "far fa-newspaper"
      href: "news/index.html"
    - text: "Source Code"
      icon: "fab fa-github"
      href: "https://github.com/msberends/AMR"

reference:
  - title: "Introduction to the package"
    desc: >
      Please find the introduction to (and some general information about) our package here.
    contents:
    - "`AMR`"
    
  - title: "Preparing data: microorganisms"
    desc: >
      These functions are meant to get taxonomically valid properties of microorganisms from any input, but
      also properties derived from taxonomy, such as the Gram stain (`mo_gramstain()`) , or `mo_is_yeast()`.
      Use `mo_source()` to teach this package how to translate your own codes to valid microorganisms, and
      use `add_custom_microorganisms() to add your own custom microorganisms to this package.
    contents:
    - "`as.mo`"
    - "`mo_property`"
    - "`add_custom_microorganisms`"
    - "`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 results"
    desc: >
      With `as.mic()` and `as.disk()` you can transform your raw input to valid MIC or disk diffusion values.
      Use `as.sir()` for cleaning raw data to let it only contain "R", "I" and "S", or to interpret MIC or disk diffusion values as SIR 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.sir`"
    - "`as.mic`"
    - "`as.disk`"
    - "`eucast_rules`"
    - "`custom_eucast_rules`"

  - title: "Analysing data"
    desc: >
      Use these function for the analysis part. You can use `susceptibility()` or `resistance()` on any antibiotic column.
      With `antibiogram()`, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination
      antibiogram(WISCA). This function also comes with support for R Markdown and Quarto.
      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:
    - "`antibiogram`"
    - "`proportion`"
    - "`count`"
    - "`is_new_episode`"
    - "`first_isolate`"
    - "`key_antimicrobials`"
    - "`mdro`"
    - "`count`"
    - "`bug_drug_combinations`"
    - "`antibiotic_class_selectors`"
    - "`mean_amr_distance`"
    - "`resistance_predict`"
    - "`guess_ab_col`"
    
  - title: "Plotting data"
    desc: >
      Use these functions for the plotting part. The `scale_*_mic()` functions extend the ggplot2 package to allow plotting of 
      MIC values, even within a manually set range.
      If using `plot()` (base R) or `autoplot()` (ggplot2) on MIC values or disk diffusion values, the user can
      set the interpretation guideline to give the bars the right SIR colours.
      The `ggplot_sir()` function is a short wrapper for users not much accustomed to ggplot2 yet.
      The `ggplot_pca()` function is a specific function to plot so-called biplots for PCA (principal component analysis).
    contents:
    - "`plot`"
    - "`ggplot_sir`"
    - "`ggplot_pca`"
    
  - title: "AMR-specific options"
    desc: >
      The AMR package is customisable, by providing settings that can be set per user or per team. For
      example, the default interpretation guideline can be changed from EUCAST to CLSI, or a supported
      language can be set for the whole team (system-language independent) for antibiotic names in a
      foreign language.
    contents:
    - "`AMR-options`"
    
  - 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:
    - "`microorganisms`"
    - "`antibiotics`"
    - "`clinical_breakpoints`"
    - "`example_isolates`"
    - "`microorganisms.codes`"
    - "`microorganisms.groups`"
    - "`intrinsic_resistant`"
    - "`dosage`"
    - "`WHOCC`"
    - "`example_isolates_unclean`"
    - "`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`"
    - "`export_ncbi_biosample`"
    - "`availability`"
    - "`get_AMR_locale`"
    - "`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`"