We can now add the interpretation of MDR-TB to our data set. You can
use:
@@ -454,40 +454,40 @@ Unique: 5
| 1 |
Mono-resistant |
-3243 |
-64.86% |
-3243 |
-64.86% |
+3193 |
+63.86% |
+3193 |
+63.86% |
| 2 |
Negative |
-946 |
-18.92% |
-4189 |
-83.78% |
+989 |
+19.78% |
+4182 |
+83.64% |
| 3 |
Multi-drug-resistant |
-439 |
-8.78% |
-4628 |
-92.56% |
+451 |
+9.02% |
+4633 |
+92.66% |
| 4 |
Poly-resistant |
-272 |
-5.44% |
-4900 |
-98.00% |
+270 |
+5.40% |
+4903 |
+98.06% |
| 5 |
Extensively drug-resistant |
-100 |
-2.00% |
+97 |
+1.94% |
5000 |
100.00% |
diff --git a/articles/PCA.html b/articles/PCA.html
index 9599e418..76a66020 100644
--- a/articles/PCA.html
+++ b/articles/PCA.html
@@ -38,7 +38,7 @@
AMR (for R)
- 2.1.1.9008
+ 2.1.1.9009
-
AMR 2.1.1.9008
+
AMR 2.1.1.9009
(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, 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
-
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
+
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.
-
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.
diff --git a/pkgdown.yml b/pkgdown.yml
index ebc982d7..218d5aba 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: 2024-02-24T17:55Z
+last_built: 2024-02-24T18:29Z
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 235480e1..32cc294c 100644
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@@ -10,7 +10,7 @@
AMR (for R)
- 2.1.1.9008
+ 2.1.1.9009