# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2022 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # 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. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # title: "AMR (for R)" url: "https://msberends.github.io/AMR/" template: bootstrap: 5 bootswatch: "flatly" assets: "pkgdown/logos" # use logos in this folder bslib: code_font: {google: "Fira Code"} body-text-align: "justify" line-height-base: 1.75 # the green "success" colour of this bootstrap theme should be the same as the green in our logo success: "#128f76" link-color: "#128f76" navbar-padding-y: "0.5rem" opengraph: twitter: creator: "@msberends" site: "@univgroningen" card: summary_large_image news: one_page: true cran_dates: true footer: structure: left: [devtext] right: [logo] components: devtext: 'AMR (for R). Developed at the University of Groningen in collaboration with non-profit organisations
Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.' logo: '' home: sidebar: structure: [toc, links, authors, citation] 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: "Data sets for download / own use" icon: "fa-database" href: "articles/datasets.html" - text: "Conduct principal component analysis for AMR" icon: "fa-compress" href: "articles/PCA.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 an article - text: "Get properties of an antibiotic" icon: "fa-capsules" href: "reference/ab_property.html" # reference instead of an article - text: "Other: benchmarks" icon: "fa-shipping-fast" href: "articles/benchmarks.html" - text: "Manual" icon: "fa-book-open" href: "reference/index.html" - text: "Authors" icon: "fa-users" href: "authors.html" - text: "Changelog" icon: "far fa-newspaper" href: "news/index.html" right: - text: "Source Code" icon: "fab fa-github" href: "https://github.com/msberends/AMR" # - text: "Survey" # icon: "fa-clipboard-list" # href: "survey.html" reference: - title: "Preparing data: microorganisms" desc: > These functions are meant to get taxonomically valid properties of microorganisms from any input. Use `mo_source()` to teach this package how to translate your own codes to valid microorganism codes. contents: - "`as.mo`" - "`mo_property`" - "`mo_source`" - title: "Preparing data: antibiotics" desc: > Use these functions to get valid properties of antibiotics from any input or to clean your input. You can even retrieve drug names and doses from clinical text records, using `ab_from_text()`. contents: - "`as.ab`" - "`ab_property`" - "`ab_from_text`" - "`atc_online_property`" - title: "Preparing data: antimicrobial resistance" desc: > With `as.mic()` and `as.disk()` you can transform your raw input to valid MIC or disk diffusion values. Use `as.rsi()` for cleaning raw data to let it only contain "R", "I" and "S", or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying [EUCAST rules](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) with `eucast_rules()`. contents: - "`as.rsi`" - "`as.mic`" - "`as.disk`" - "`eucast_rules`" - "`custom_eucast_rules`" - title: "Analysing data: antimicrobial resistance" desc: > Use these function for the analysis part. You can use `susceptibility()` or `resistance()` on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using `first_isolate()` or `is_new_episode()`. You can also filter your data on certain resistance in certain antibiotic classes (`carbapenems()`, `aminoglycosides()`), or determine multi-drug resistant microorganisms (MDRO, `mdro()`). contents: - "`proportion`" - "`count`" - "`is_new_episode`" - "`first_isolate`" - "`key_antimicrobials`" - "`mdro`" - "`count`" - "`plot`" - "`ggplot_rsi`" - "`bug_drug_combinations`" - "`antibiotic_class_selectors`" - "`resistance_predict`" - "`guess_ab_col`" - title: "Background information on included data" 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`" - "`example_isolates`" - "`microorganisms`" - "`microorganisms.codes`" - "`microorganisms.old`" - "`antibiotics`" - "`intrinsic_resistant`" - "`dosage`" - "`catalogue_of_life`" - "`catalogue_of_life_version`" - "`WHOCC`" - "`example_isolates_unclean`" - "`rsi_translation`" - "`WHONET`" - title: "Other: miscellaneous 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: - "`age_groups`" - "`age`" - "`availability`" - "`get_AMR_locale`" - "`ggplot_pca`" - "`italicise_taxonomy`" - "`join`" - "`like`" - "`mo_matching_score`" - "`pca`" - "`random`" - title: "Other: statistical tests" desc: > Some statistical tests or methods are not part of base R and were added to this package for convenience. contents: - "`g.test`" - "`kurtosis`" - "`skewness`" - title: "Other: 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`"