-
AMR 2.1.1.9274
+
AMR 2.1.1.9275
(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.)
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.
-
tl;dr
+
tl;dr
- Scope Expansion: One Health support (Human + Veterinary + Environmental microbiology).
- Data Updates:
-
Full Changelog
+
Full Changelog
-
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.
- Functions
resistance_predict() and sir_predict() are 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.
@@ -170,7 +170,7 @@
-
Changed
+
Changed
- SIR interpretation
- Support for parallel computing to greatly improve speed using the
parallel package (part of base R). Use as.sir(your_data, parallel = TRUE) to run SIR interpretation using multiple cores.
- It is now possible to use column names for arguments
guideline, ab, mo, and uti: as.sir(..., ab = "column1", mo = "column2", uti = "column3"). This greatly improves the flexibility for users.
@@ -249,11 +249,12 @@
- MDRO determination (using
mdro())
- Implemented the new Dutch national MDRO guideline (SRI-richtlijn BRMO, Nov 2024)
- Added arguments
esbl, carbapenemase, mecA, mecC, vanA, vanB to denote column names or logical values indicating presence of these genes (or production of their proteins)
+- The Verbose Mode (
verbose = TRUE) now includes the guideline name
- Added console colours support of
sir class for Positron
-
Other
+
Other
- New website domain: https://amr-for-r.org! The old domain will remain to work.
- 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
@@ -264,7 +265,7 @@
-
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 df8bbde8d..d83ca8f11 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
-last_built: 2025-05-12T10:39Z
+last_built: 2025-05-13T17:01Z
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 479b77224..eac8406b2 100644
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -7,7 +7,7 @@
AMR (for R)
- 2.1.1.9274
+ 2.1.1.9275