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Package: AMR
Version: 2.1.1.9009
Date: 2024-02-24
Version: 2.1.1.9010
Date: 2024-02-25
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

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NEWS.md
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# AMR 2.1.1.9009
# AMR 2.1.1.9010
*(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!)*
## A New Milestone: One Health Support (= Human + Veterinary + Environmental)
#### A New Milestone: One Health Support (= Human + Veterinary + Environmental)
This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the [University of Prince Edward Island](https://www.upei.ca/avc), Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
* `as.sir()` now supports animal breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html).
* The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
* `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
* `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
## Breaking
* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over a year ago
## New functions
* The group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
* `limit_mic_range()`, which allows to limit MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
## New
* The function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
* Function `limit_mic_range()`, which allows to limit MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
* One Health implementation
* Function `as.sir()` now supports animal breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
* The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html).
* The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
* `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
* `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
### Changed
## Changed
* For MICs:
* Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
* Added new argument `keep_operators` to `as.mic()`. This can be `"all"` (default), `"none"`, or `"edges"`. This argument is also available in the new `limit_mic_range()` and `scale_*_mic()` functions.
@ -26,6 +27,9 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Updated all ATC codes from WHOCC
* Updated all antibiotic DDDs from WHOCC
## Other
* Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
# AMR 2.1.1

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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>
* Provides an **all-in-one solution** for AMR data analysis in a One Health approach
* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
* Provides the **full microbiological taxonomy** and data on **all antimicrobial drugs**
* Applies all recent **CLSI and EUCAST clinical breakpoints** for MICs and disk zones
* Applies all recent **CLSI and EUCAST clinical and veterinary breakpoints** for MICs and disk zones
* Corrects for duplicate isolates, **calculates and predicts AMR** per antibiotic class
* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC** and **SNOMED CT**
* Works on Windows, macOS and Linux with **all versions of R** since R-3.0 and is completely **dependency-free**, highly suitable for places with **limited resources**

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{
"name": "AMR (for R)",
"short_name": "AMR (for R)",
"name": "AMR for R",
"short_name": "AMR for R",
"icons": [
{
"src": "/android-chrome-192x192.png?v=2",
"src": "/android-chrome-192x192.png?v=newlogo",
"sizes": "192x192",
"type": "image/png"
},
{
"src": "/android-chrome-512x512.png?v=2",
"src": "/android-chrome-512x512.png?v=newlogo",
"sizes": "512x512",
"type": "image/png"
}
],
"theme_color": "#ffffff",
"background_color": "#ffffff",
"start_url": "https://msberends.github.io/AMR/",
"theme_color": "#128f76",
"background_color": "#128f76",
"display": "standalone"
}

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