mirror of https://github.com/msberends/AMR.git
214 lines
7.8 KiB
YAML
214 lines
7.8 KiB
YAML
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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title: "AMR (for R)"
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url: "https://msberends.github.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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cran_dates: 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: "Data sets for download / own use"
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icon: "fa-database"
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href: "articles/datasets.html"
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- text: "Conduct principal component analysis for AMR"
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icon: "fa-compress"
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href: "articles/PCA.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 an 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 an 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/index.html"
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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/index.html"
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right:
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- text: "Source Code"
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icon: "fab fa-github"
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href: "https://github.com/msberends/AMR"
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# - text: "Survey"
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# icon: "fa-clipboard-list"
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# href: "survey.html"
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reference:
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- title: "Preparing data: microorganisms"
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desc: >
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These functions are meant to get taxonomically valid properties of microorganisms from any input.
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Use `mo_source()` to teach this package how to translate your own codes to valid microorganism codes.
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contents:
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- "`as.mo`"
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- "`mo_property`"
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- "`mo_source`"
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- title: "Preparing data: antibiotics"
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desc: >
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Use these functions to get valid properties of antibiotics from any input or to clean your input.
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You can even retrieve drug names and doses from clinical text records, using `ab_from_text()`.
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contents:
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- "`as.ab`"
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- "`ab_property`"
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- "`ab_from_text`"
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- "`atc_online_property`"
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- title: "Preparing data: antimicrobial resistance"
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desc: >
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With `as.mic()` and `as.disk()` you can transform your raw input to valid MIC or disk diffusion values.
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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.
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Afterwards, you can extend antibiotic interpretations by applying [EUCAST rules](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) with `eucast_rules()`.
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contents:
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- "`as.rsi`"
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- "`as.mic`"
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- "`as.disk`"
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- "`eucast_rules`"
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- "`custom_eucast_rules`"
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- title: "Analysing data: antimicrobial resistance"
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desc: >
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Use these function for the analysis part. You can use `susceptibility()` or `resistance()` on any antibiotic column.
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Be sure to first select the isolates that are appropiate for analysis, by using `first_isolate()` or `is_new_episode()`.
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You can also filter your data on certain resistance in certain antibiotic classes (`carbapenems()`, `aminoglycosides()`), or determine multi-drug resistant microorganisms (MDRO, `mdro()`).
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contents:
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- "`proportion`"
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- "`count`"
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- "`is_new_episode`"
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- "`first_isolate`"
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- "`key_antimicrobials`"
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- "`mdro`"
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- "`count`"
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- "`plot`"
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- "`ggplot_rsi`"
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- "`bug_drug_combinations`"
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- "`antibiotic_class_selectors`"
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- "`resistance_predict`"
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- "`guess_ab_col`"
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- title: "Background information on included data"
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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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- "`example_isolates`"
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- "`microorganisms`"
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- "`microorganisms.codes`"
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- "`microorganisms.old`"
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- "`antibiotics`"
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- "`intrinsic_resistant`"
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- "`dosage`"
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- "`catalogue_of_life`"
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- "`catalogue_of_life_version`"
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- "`WHOCC`"
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- "`lifecycle`"
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- "`example_isolates_unclean`"
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- "`rsi_translation`"
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- "`WHONET`"
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- title: "Other: miscellaneous 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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- "`age_groups`"
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- "`age`"
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- "`availability`"
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- "`get_AMR_locale`"
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- "`ggplot_pca`"
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- "`italicise_taxonomy`"
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- "`join`"
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- "`like`"
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- "`mo_matching_score`"
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- "`pca`"
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- "`random`"
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- title: "Other: statistical tests"
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desc: >
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Some statistical tests or methods are not part of base R and were added to this package for convenience.
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contents:
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- "`g.test`"
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- "`kurtosis`"
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- "`skewness`"
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- title: "Other: deprecated functions"
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desc: >
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These functions are deprecated, meaning that they will 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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template:
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bootstrap: 3
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opengraph:
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twitter:
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creator: "@msberends"
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site: "@univgroningen"
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card: summary_large_image
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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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