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AMR/_pkgdown.yml

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# ==================================================================== #
# 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). Developed at the <a target="_blank" href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl">University Medical Center Groningen</a>.'
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>'
home:
sidebar:
structure: [toc, links, authors, citation]
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: "Other: benchmarks"
# icon: "fa-shipping-fast"
# href: "articles/benchmarks.html"
- 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: "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`"
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