-
AMR 2.1.1.9285
+
AMR 2.1.1.9287
(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
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- Scope Expansion: One Health support (Human + Veterinary + Environmental microbiology).
-- Data Updates:
-
-
-
antibiotics renamed to antimicrobials.
-- Veterinary antimicrobials and WHOCC codes added.
-- MycoBank fungal taxonomy integrated (+20,000 fungi).
-
-- Breakpoints & Interpretations:
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- CLSI/EUCAST 2024-2025 breakpoints added; EUCAST 2025 default.
--
-
as.sir() supports NI/SDD levels; parallel computation enabled.
-- Custom S/I/R/SDD/NI definitions allowed.
-- Improved handling of capped MICs.
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-- New Tools & Functions:
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-- Predictive Modelling:
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-- Python Compatibility: AMR R package now runs in Python.
-- Selector Improvements:
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-- MIC/Disks Handling:
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- MIC strict comparisons, added levels.
-- Disk diffusion range expanded (0–50 mm).
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-- EUCAST Rules and MDROs:
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- EUCAST v12–v15 rules implemented.
-- Dutch MDRO 2024 guideline support in
mdro().
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-- Infrastructure:
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- New website: https://amr-for-r.org.
-- Improved
vctrs integration for tidyverse workflows.
-- Dropped SAS
.xpt file support.
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-- Other Fixes & Enhancements:
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- Support for 8 new languages, adding to a total of 28 languages.
-- Faster microorganism identification.
-- Improved antimicrobial and MIC handling.
-- Extended documentation, additional contributors acknowledged.
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-
-
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Full Changelog
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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.
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New
+
New
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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 +118,7 @@
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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.
@@ -256,7 +204,7 @@
- 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
@@ -265,9 +213,8 @@
- Greatly updated and expanded documentation
- 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 6cb485ac7..fba3bf6fe 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,5 +1,5 @@
pandoc: 3.1.11
-pkgdown: 2.1.2
+pkgdown: 2.1.3
pkgdown_sha: ~
articles:
AMR_for_Python: AMR_for_Python.html
@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
-last_built: 2025-05-21T14:57Z
+last_built: 2025-06-01T10:21Z
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 6211f7727..f8df8f286 100644
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -7,7 +7,7 @@
AMR (for R)
- 2.1.1.9285
+ 2.1.1.9287
-
-
An object of class tbl_df (inherits from tbl, data.frame) with 497 rows and 14 columns.
-