new logo
@ -1,6 +1,6 @@
|
||||
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
|
||||
|
26
NEWS.md
@ -1,23 +1,24 @@
|
||||
# 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
|
||||
|
||||
|
@ -35,7 +35,11 @@ template:
|
||||
bootswatch: "flatly"
|
||||
assets: "pkgdown/logos" # use logos in this folder
|
||||
bslib:
|
||||
base_font: {google: "Lato"}
|
||||
heading_font: {google: " Lato"}
|
||||
code_font: {google: "Fira Code"}
|
||||
navbar-bg: "#a8d5ef"
|
||||
nav-link-color: "#212529"
|
||||
# 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
|
||||
|
3
data-raw/AMR new logo.txt
Normal file
@ -0,0 +1,3 @@
|
||||
green grass #a7dbc3
|
||||
green bacteria #128F76
|
||||
blue sky #a8d5ef
|
3335
data-raw/logo.old.svg
Normal file
After Width: | Height: | Size: 164 KiB |
3901
data-raw/logo.svg
Before Width: | Height: | Size: 164 KiB After Width: | Height: | Size: 171 KiB |
3
index.md
@ -1,8 +1,9 @@
|
||||
# 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**
|
||||
|
3901
logo.svg
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Before Width: | Height: | Size: 3.6 KiB After Width: | Height: | Size: 9.1 KiB |
Before Width: | Height: | Size: 9.7 KiB After Width: | Height: | Size: 9.8 KiB |
@ -2,9 +2,9 @@
|
||||
<browserconfig>
|
||||
<msapplication>
|
||||
<tile>
|
||||
<square150x150logo src="/mstile-150x150.png?v=2"/>
|
||||
<square310x310logo src="/mstile-310x310.png?v=2"/>
|
||||
<TileColor>#eeeeee</TileColor>
|
||||
<square150x150logo src="/mstile-150x150.png?v=newlogo"/>
|
||||
<square310x310logo src="/mstile-310x310.png?v=newlogo"/>
|
||||
<TileColor>#128f76</TileColor>
|
||||
</tile>
|
||||
</msapplication>
|
||||
</browserconfig>
|
||||
|
Before Width: | Height: | Size: 1.2 KiB After Width: | Height: | Size: 1.4 KiB |
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Before Width: | Height: | Size: 23 KiB After Width: | Height: | Size: 52 KiB |
@ -2,94 +2,511 @@
|
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<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 20010904//EN"
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"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">
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<svg version="1.0" xmlns="http://www.w3.org/2000/svg"
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width="792.000000pt" height="792.000000pt" viewBox="0 0 792.000000 792.000000"
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width="714.000000pt" height="714.000000pt" viewBox="0 0 714.000000 714.000000"
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preserveAspectRatio="xMidYMid meet">
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<metadata>
|
||||
Created by potrace 1.14, written by Peter Selinger 2001-2017
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||||
</metadata>
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||||
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@ -1,20 +1,19 @@
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{
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"name": "AMR (for R)",
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"short_name": "AMR (for R)",
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"name": "AMR for R",
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}
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],
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"start_url": "https://msberends.github.io/AMR/",
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Before Width: | Height: | Size: 164 KiB After Width: | Height: | Size: 171 KiB |