mirror of https://github.com/msberends/AMR.git
191 lines
6.5 KiB
YAML
191 lines
6.5 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.gitlab.io/AMR. #
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# ==================================================================== #
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title: "AMR (for R)"
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url: "https://msberends.gitlab.io/AMR"
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development:
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mode: "release" # improves indexing by search engines
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version_tooltip: "Latest development version"
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news:
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one_page: true
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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/resistance_predict.html"
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- text: "Determine multi-drug resistance (MDR)"
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icon: "fa-skull-crossbones"
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href: "articles/MDR.html"
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- text: "Work with WHONET data"
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icon: "fa-globe-americas"
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href: "articles/WHONET.html"
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- text: "Import data from SPSS/SAS/Stata"
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icon: "fa-file-upload"
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href: "articles/SPSS.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: "reference/mo_property.html" # reference instead of article
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- text: "Get properties of an antibiotic"
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icon: "fa-capsules"
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href: "reference/ab_property.html" # reference instead of article
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- text: "Other: benchmarks"
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icon: "fa-shipping-fast"
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href: "articles/benchmarks.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: "Background information"
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desc: >
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Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
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for more information about how to work with functions in this package.
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contents:
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- "`AMR`"
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- "`catalogue_of_life`"
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- "`catalogue_of_life_version`"
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- "`WHOCC`"
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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 to add
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variables later on (like taxonomic properties) or to fix and extend
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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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- "`mo_source`"
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- "`eucast_rules`"
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- "`rsi_translation`"
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- "`guess_ab_col`"
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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, multi-drug resistant microorganisms (MDRO), getting
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properties of microorganisms or antibiotics and determining the age of
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patients or divide ages into age groups.
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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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- "`age`"
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- "`age_groups`"
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- "`p.symbol`"
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- "`join`"
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- "`atc_online_property`"
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- title: "Analysing your data"
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desc: >
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Functions for conducting AMR analysis, like counting isolates, calculating
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resistance or susceptibility, or make plots.
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contents:
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- "`availability`"
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- "`count`"
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- "`portion`"
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- "`filter_ab_class`"
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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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- "`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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- "`WHONET`"
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- "`microorganisms.codes`"
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- "`microorganisms.old`"
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- title: Other functions
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desc: >
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These functions are mostly for internal use, but some of
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them may also be suitable for your analysis. Especially the
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'like' function can be useful: `if (x %like% y) {...}`.
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contents:
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- "`get_locale`"
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- "`like`"
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- title: Extended functions
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desc: >
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These functions are extensions of functions in other packages.
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contents:
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- "`extended-functions`"
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- title: functions
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desc: >
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These functions are deprecated, meaning that they still
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work but show a warning with every use and will be removed
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in a future version.
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contents:
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- "`AMR-deprecated`"
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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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