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(v2.1.1.9051) fix VGS mo code
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Package: AMR
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Version: 2.1.1.9050
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Date: 2024-06-15
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Version: 2.1.1.9051
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Date: 2024-06-16
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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NEWS.md
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NEWS.md
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# AMR 2.1.1.9050
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# AMR 2.1.1.9051
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*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*
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"VFL" "B_VIBRI_FLVL"
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"VFU" "B_VIBRI_FRNS"
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"VGC" "B_VGCCC"
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"VGS" "B_VGCCC_SLMN"
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"VHI" "B_VIBRI_CHLR"
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"VHO" "B_GRMNT_HLLS"
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"VI-" "B_VIBRI"
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index.md
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index.md
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# The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
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* Provides an **all-in-one solution** for AMR data analysis in a One Health approach
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* Used in over 175 countries, translated into 20 languages
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* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
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* Used in over 175 countries, available in 20 languages
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* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
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* Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
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* Applies all recent **CLSI** and **EUCAST** clinical and veterinary breakpoints for MICs and disk zones
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@ -26,7 +26,7 @@ This work was published in the Journal of Statistical Software (Volume 104(3); [
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After installing this package, R knows [**~52,000 distinct microbial species**](./reference/microorganisms.html) (updated December 2022) and all [**~600 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl).
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##### Used in over 175 countries, translated into 20 languages
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##### Used in over 175 countries, available in 20 languages
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<a href="./countries_large.png" target="_blank"><img src="./countries.png" align="right" style="max-width: 300px;" /></a>
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\docType{data}
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\name{microorganisms.codes}
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\alias{microorganisms.codes}
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\title{Data Set with 4 972 Common Microorganism Codes}
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\title{Data Set with 4 971 Common Microorganism Codes}
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\format{
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A \link[tibble:tibble]{tibble} with 4 972 observations and 2 variables:
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A \link[tibble:tibble]{tibble} with 4 971 observations and 2 variables:
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\itemize{
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\item \code{code}\cr Commonly used code of a microorganism. \emph{This is a unique identifier.}
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\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
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