# ==================================================================== # # 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: "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: "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.") - "`eucast_rules`" - "`guess_ab_col`" - "`mo_source`" - "`read.4D`" - "`rsi_translation`" - title: "Enhancing your data" desc: > Functions to add new data to your existing data, such as 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: - "`ab_property`" - "`age_groups`" - "`age`" - "`atc_online_property`" - "`first_isolate`" - "`join`" - "`key_antibiotics`" - "`mdro`" - "`mo_property`" - "`p_symbol`" - title: "Analysing your data" desc: > Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, or make plots. contents: - "`availability`" - "`bug_drug_combinations`" - "`count`" - "`filter_ab_class`" - "`g.test`" - "`ggplot_rsi`" - "`kurtosis`" - "`portion`" - "`resistance_predict`" - "`skewness`" - title: "Included data sets" desc: > Scientifically reliable references for microorganisms and antibiotics, and example data sets to use for practise. contents: - "`antibiotics`" - "`antivirals`" - "`example_isolates`" - "`microorganisms.codes`" - "`microorganisms.old`" - "`microorganisms`" - "`WHONET`" - 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: 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`" - "`extended-functions`" - "`like`" - "`reexports`" - title: 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`" 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/ Alexander W Friedrich: href: https://www.rug.nl/staff/a.w.friedrich/ Bhanu N M Sinha: href: https://www.rug.nl/staff/b.sinha/ Casper J Albers: href: https://www.rug.nl/staff/c.j.albers/ Corinna Glasner: href: https://www.rug.nl/staff/c.glasner/ template: assets: "pkgdown/logos" # use logos in this folder params: noindex: false bootswatch: "flatly" docsearch: # using algolia.com api_key: "f737050abfd4d726c63938e18f8c496e" index_name: "amr"