@@ -455,7 +455,7 @@ model.
into a structured time-series format.
# Load required libraries
-library(AMR)
+library(AMR)
library(tidymodels)
# Transform dataset
diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index ffe0dda2e..fc1efea79 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -31,7 +31,7 @@
AMR (for R)
- 2.1.1.9235
+ 2.1.1.9236
Partners
diff --git a/news/index.html b/news/index.html
index 65537e799..716a3494f 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
AMR (for R)
- 2.1.1.9235
+ 2.1.1.9236
-
AMR 2.1.1.9235
-
(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! Install this beta using the instructions here.)
+
AMR 2.1.1.9236
+
(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! Install this beta using the instructions here.)
-
A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)
+
A New Milestone: AMR v3.0 with 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’s Atlantic Veterinary College, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
-
Breaking
+
Breaking
- Dataset
antibiotics has been renamed to antimicrobials as the data set contains more than just antibiotics. Using antibiotics will still work, but now returns a warning.
- Removed all functions and references that used the deprecated
rsi class, which were all replaced with their sir equivalents over two years ago.
-- Function
resistance_predict() is now deprecated and will be removed in a future version. Use the tidymodels framework instead, for which we wrote a basic introduction.
+- Function
resistance_predict() is now deprecated and will be removed in a future version. Use the tidymodels framework instead, for which we wrote a basic introduction.
-
New
+
New
-
One Health implementation
- Function
as.sir() now has extensive support for veterinary 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
clinical_breakpoints data set contains all these breakpoints, and can be downloaded on our download page.
- The (new)
antimicrobials 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”)
@@ -106,7 +106,7 @@
-
Support for
tidymodels
-- All antimicrobial selectors (such as
aminoglycosides() and betalactams()) are now supported in tidymodels packages such as recipe and parsnip. See for more info our tutorial on using these AMR functions for predictive modelling.
+- All antimicrobial selectors (such as
aminoglycosides() and betalactams()) are now supported in tidymodels packages such as recipe and parsnip. See for more info our tutorial on using these AMR functions for predictive modelling.
-
Other
@@ -116,7 +116,7 @@
-
Changed
+
Changed
- SIR interpretation
- It is now possible to use column names for argument
ab, mo, and uti: as.sir(..., ab = "column1", mo = "column2", uti = "column3"). This greatly improves the flexibility for users.
- Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.
@@ -195,7 +195,7 @@
- Added console colours support of
sir class for Positron
-
Other
+
Other
- Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
- Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
- Added Prof. Kat Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes
@@ -204,7 +204,7 @@
- Stopped support for SAS (
.xpt) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.
-
Older Versions
+
Older Versions
This changelog only contains changes from AMR v3.0 (March 2025) and later.
- For prior v2 versions, please see our v2 archive.
- For prior v1 versions, please see our v1 archive.
diff --git a/pkgdown.yml b/pkgdown.yml
index 4319e5fb3..97d9560e8 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
PCA: PCA.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
-last_built: 2025-04-08T15:07Z
+last_built: 2025-04-12T15:54Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles
diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html
index 9eb9f8ffe..7e6a284e5 100644
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -7,7 +7,7 @@
AMR (for R)
- 2.1.1.9235
+ 2.1.1.9236