We can now add the interpretation of MDR-TB to our data set. You can
use:
@@ -454,40 +455,40 @@ Unique: 5
| 1 |
Mono-resistant |
-3193 |
-63.86% |
-3193 |
-63.86% |
+3177 |
+63.54% |
+3177 |
+63.54% |
| 2 |
Negative |
-989 |
-19.78% |
-4182 |
-83.64% |
+1019 |
+20.38% |
+4196 |
+83.92% |
| 3 |
Multi-drug-resistant |
-451 |
-9.02% |
-4633 |
-92.66% |
+479 |
+9.58% |
+4675 |
+93.50% |
| 4 |
Poly-resistant |
-270 |
-5.40% |
-4903 |
-98.06% |
+201 |
+4.02% |
+4876 |
+97.52% |
| 5 |
Extensively drug-resistant |
-97 |
-1.94% |
+124 |
+2.48% |
5000 |
100.00% |
diff --git a/articles/PCA.html b/articles/PCA.html
index 76a66020..763c4c15 100644
--- a/articles/PCA.html
+++ b/articles/PCA.html
@@ -15,7 +15,8 @@
-
+
+
@@ -38,7 +39,7 @@
AMR (for R)
- 2.1.1.9009
+ 2.1.1.9010
-
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)
-
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, 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. * 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
+
+
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, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
-
Breaking
+
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.
+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.
+- The
antibiotics data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
-
-
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.
-
-
Changed
+
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
- 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.
@@ -185,7 +194,10 @@
- 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
CRAN release: 2023-10-21
diff --git a/pkgdown.yml b/pkgdown.yml
index 218d5aba..a3b2643f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
other_pkg: other_pkg.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
-last_built: 2024-02-24T18:29Z
+last_built: 2024-02-25T13:43Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles
diff --git a/reference/AMR-options.html b/reference/AMR-options.html
index 32cc294c..e691df1b 100644
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@@ -1,5 +1,5 @@
-
Options for the AMR package — AMR-options • AMR (for R)Options for the AMR package — AMR-options • AMR (for R)
@@ -10,7 +10,7 @@
AMR (for R)
-
2.1.1.9009
+
2.1.1.9010