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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.gitab.io/AMR. #
# ==================================================================== #
url: 'https://msberends.gitlab.io/AMR'
title: 'AMR (for R)'
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/Predict.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 properties of a microorganism'
icon: 'fa-bug'
href: 'articles/mo_property.html'
- text: 'Get properties of an antibiotic'
icon: 'fa-capsules'
href: 'articles/ab_property.html'
- text: 'Create frequency tables'
icon: 'fa-sort-amount-down'
href: 'articles/freq.html'
- text: 'Use the G-test'
icon: 'fa-clipboard-check'
href: 'articles/G_test.html'
- 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`'
- '`ITIS`'
- '`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`'
- '`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`'
- '`atc_property`'
- '`atc_online_property`'
- '`abname`'
- '`age`'
- '`age_groups`'
- '`p.symbol`'
- '`join`'
- title: 'Analysing your data'
desc: >
Functions for conducting AMR analysis, like counting isolates, calculating
resistance or susceptibility, creating frequency tables or make plots.
contents:
- '`count`'
- '`portion`'
- '`freq`'
- '`g.test`'
- '`ggplot_rsi`'
- '`kurtosis`'
- '`resistance_predict`'
- '`rsi`'
- '`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`'
- '`microorganisms.codes`'
- '`microorganisms.old`'
- '`supplementary_data`'
- title: Other
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`'
- '`mo_failures`'
- '`mo_renamed`'
- '`ab_property`'
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'