mirror of https://github.com/msberends/AMR.git
153 lines
4.8 KiB
YAML
153 lines
4.8 KiB
YAML
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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url: https://msberends.gitlab.io/AMR
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title: 'AMR (for R)'
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navbar:
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title: 'AMR (for R)'
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left:
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- text: 'Home'
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icon: 'fa-home'
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href: 'index.html'
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- text: 'How to'
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icon: 'fa-question-circle'
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menu:
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- text: 'Conduct AMR analysis'
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icon: 'fa-directions'
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href: 'articles/AMR.html'
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- text: 'Predict antimicrobial resistance'
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icon: 'fa-dice'
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href: 'articles/Predict.html'
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- text: 'Apply EUCAST rules'
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icon: 'fa-exchange-alt'
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href: 'articles/EUCAST.html'
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- text: 'Get properties of a microorganism'
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icon: 'fa-bug'
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href: 'articles/mo_property.html'
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- text: 'Get properties of an antibiotic'
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icon: 'fa-capsules'
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href: 'articles/ab_property.html'
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- text: 'Create frequency tables'
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icon: 'fa-sort-amount-down'
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href: 'articles/freq.html'
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- text: 'Use the G-test'
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icon: 'fa-clipboard-check'
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href: 'articles/G_test.html'
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- text: 'Manual'
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icon: 'fa-book-open'
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href: 'reference/'
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- text: 'Authors'
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icon: 'fa-users'
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href: 'authors.html'
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- text: 'Changelog'
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icon: 'far fa-newspaper'
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href: 'news/'
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right:
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- text: 'Source Code'
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icon: 'fab fa-gitlab'
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href: 'https://gitlab.com/msberends/AMR'
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- text: 'Licence'
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icon: 'fa-book'
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href: 'LICENSE-text.html'
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reference:
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- title: Cleaning your data
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desc: >
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Functions for cleaning and optimising your data, to be able
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to add variables later on (like taxonomic properties) or to
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fix and extend antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
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contents:
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- starts_with("as.")
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- '`eucast_rules`'
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- '`read.4D`'
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- title: Adding variables to your data
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desc: >
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Functions to add new data to existing data, like the determination
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of first isolates,
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contents:
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- '`first_isolate`'
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- '`mdro`'
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- '`key_antibiotics`'
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- '`mo_property`'
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- '`ab_property`'
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- '`atc_property`'
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- '`abname`'
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- '`age`'
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- '`age_groups`'
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- '`p.symbol`'
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- '`join`'
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- title: Analysing your data
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desc: >
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Functions for conducting AMR analysis
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contents:
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- '`count`'
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- '`portion`'
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- '`freq`'
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- '`g.test`'
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- '`ggplot_rsi`'
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- '`kurtosis`'
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- '`resistance_predict`'
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- '`rsi`'
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- '`skewness`'
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- title: Included data sets
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desc: >
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References for microorganisms and antibiotics, and even a
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genuine data set with isolates from septic patients.
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contents:
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- '`antibiotics`'
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- '`microorganisms`'
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- '`septic_patients`'
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- '`microorganisms.certe`'
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- '`microorganisms.old`'
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- '`microorganisms.umcg`'
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- '`supplementary_data`'
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- title: Other
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desc: ~
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contents:
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- '`get_locale`'
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- '`like`'
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- '`mo_failures`'
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- '`mo_renamed`'
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authors:
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Matthijs S. Berends:
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href: https://www.rug.nl/staff/m.s.berends/
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Christian F. Luz:
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href: https://www.rug.nl/staff/c.f.luz/
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Corinna Glasner:
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href: https://www.rug.nl/staff/c.glasner/
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Alex W. Friedrich:
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href: https://www.rug.nl/staff/a.w.friedrich/
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Bhanu N. M. Sinha:
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href: https://www.rug.nl/staff/b.sinha/
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template:
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assets: pkgdown/logos # use logos in this folder
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params:
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noindex: false
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bootswatch: flatly
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docsearch:
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# using algolia.com
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api_key: 'f737050abfd4d726c63938e18f8c496e'
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index_name: 'amr'
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