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AMR/_pkgdown.yml

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# 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. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
title: "AMR (for R)"
url: "https://msberends.gitlab.io/AMR"
development:
mode: "release" # improves indexing by search engines
version_tooltip: "Latest development version"
news:
one_page: true
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: "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 article
- text: "Get properties of an antibiotic"
icon: "fa-capsules"
href: "reference/ab_property.html" # reference instead of article
- text: "Create frequency tables"
icon: "fa-sort-amount-down"
href: "articles/freq.html"
# - text: "Use the G-test"
# icon: "fa-clipboard-check"
# href: "reference/g.test.html" # reference instead of article
- text: "Other: benchmarks"
icon: "fa-shipping-fast"
href: "articles/benchmarks.html"
- text: "Manual"
icon: "fa-book-open"
href: "reference/"
- text: "Authors"
icon: "fa-users"
href: "authors.html"
- text: "Changelog"
icon: "far fa-newspaper"
href: "news/"
right:
- text: "Source Code"
icon: "fab fa-gitlab"
href: "https://gitlab.com/msberends/AMR"
- text: "Licence"
icon: "fa-book"
href: "LICENSE-text.html"
reference:
- title: "Background information"
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`"
- "`catalogue_of_life`"
- "`catalogue_of_life_version`"
- "`WHOCC`"
- title: "Cleaning your data"
desc: >
Functions for cleaning and optimising your data, to be able to add
variables later on (like taxonomic properties) or to fix and extend
antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
contents:
- starts_with("as.")
- "`mo_source`"
- "`eucast_rules`"
- "`rsi_translation`"
- "`guess_ab_col`"
- "`read.4D`"
- title: "Adding variables to your data"
desc: >
Functions to add new data to existing data, like the determination
of first isolates, multi-drug resistant microorganisms (MDRO), getting
properties of microorganisms or antibiotics and determining the age of
patients or divide ages into age groups.
contents:
- "`first_isolate`"
- "`mdro`"
- "`key_antibiotics`"
- "`mo_property`"
- "`ab_property`"
- "`age`"
- "`age_groups`"
- "`p.symbol`"
- "`join`"
- "`atc_online_property`"
- title: "Analysing your data"
desc: >
Functions for conducting AMR analysis, like counting isolates, calculating
resistance or susceptibility, creating frequency tables or make plots.
contents:
- "`availability`"
- "`count`"
- "`portion`"
- "`filter_ab_class`"
- "`freq`"
- "`g.test`"
- "`ggplot_rsi`"
- "`kurtosis`"
- "`resistance_predict`"
- "`skewness`"
- title: "Included data sets"
desc: >
References for microorganisms and antibiotics, and even a
genuine data set with isolates from septic patients.
contents:
- "`antibiotics`"
- "`microorganisms`"
- "`septic_patients`"
- "`WHONET`"
- "`microorganisms.codes`"
- "`microorganisms.old`"
- title: Other 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:
- "`get_locale`"
- "`like`"
- title: Extended functions
desc: >
These functions are extensions of functions in other packages.
contents:
- "`extended-functions`"
- title: functions
desc: >
These functions are deprecated, meaning that they still
work but show a warning with every use and will be removed
in a future version.
contents:
- "`AMR-deprecated`"
authors:
Matthijs S. Berends:
href: https://www.rug.nl/staff/m.s.berends/
Christian F. Luz:
href: https://www.rug.nl/staff/c.f.luz/
Corinna Glasner:
href: https://www.rug.nl/staff/c.glasner/
Alex W. Friedrich:
href: https://www.rug.nl/staff/a.w.friedrich/
Bhanu N. M. Sinha:
href: https://www.rug.nl/staff/b.sinha/
template:
assets: "pkgdown/logos" # use logos in this folder
params:
noindex: false
bootswatch: "flatly"
docsearch:
# using algolia.com
api_key: "f737050abfd4d726c63938e18f8c496e"
index_name: "amr"
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