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# ==================================================================== #
# 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/"
template:
bootstrap: 5
includes: # support for mathematical formulas, from https://github.com/r-lib/pkgdown/issues/2704#issuecomment-2307055568
in_header: |
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous">
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script>
<script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script>
bootswatch: "flatly"
# dark mode: the CSS in pkgdown/extra.css is prepared for it, but light mode is enforced for now
light-switch: false
bslib:
base_font: {google: "Lato"}
heading_font: {google: "Lato"}
code_font: {google: "Fira Code"}
# body-text-align: "justify" # this is now only in `p {}` in extra.css
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 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`"
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