# ==================================================================== # # 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_label: default 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: 'articles/mo_property.html' href: 'reference/mo_property.html' - text: 'Get properties of an antibiotic' icon: 'fa-capsules' # href: 'articles/ab_property.html' href: 'reference/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`' - '`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: Deprecated 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'