-
AMR 2.1.1.9220
+
AMR 2.1.1.9221
(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.
-
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.
@@ -114,11 +114,12 @@
-
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.
- To get quantitative values,
as.double() on a sir object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become NA). Other functions using sir classes (e.g., summary()) are updated to reflect the change to contain NI and SDD.
+- Combined MIC values (e.g., from CLSI) are now supported
- The argument
conserve_capped_values in as.sir() has been replaced with capped_mic_handling, which allows greater flexibility in handling capped MIC values (<, <=, >, >=). The four available options ("standard", "strict", "relaxed", "inverse") provide full control over whether these values should be interpreted conservatively or ignored. Using conserve_capped_values is now deprecated and returns a warning.
-
@@ -188,7 +189,7 @@
- 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
- Greatly improved
vctrs integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as dplyr’s bind_rows(), rowwise() and c_across() are now supported for e.g. columns of class mic. Despite this, this AMR package is still zero-dependent on any other package, including dplyr and vctrs.
@@ -196,7 +197,7 @@
- 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 991f814be..2ded9e32b 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
-last_built: 2025-03-19T15:19Z
+last_built: 2025-03-20T20:51Z
urls:
reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles
diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html
index 838486f87..c9d7bb21c 100644
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -7,7 +7,7 @@
AMR (for R)
- 2.1.1.9220
+ 2.1.1.9221