-
AMR 2.1.1.9077
+
AMR 2.1.1.9078
(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
- Removed all functions and references that used the deprecated
rsi class, which were all replaced with their sir equivalents over a year ago
-
New
+
New
- One Health implementation
- Function
as.sir() now has extensive support for 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.
@@ -101,13 +101,19 @@
-
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.
-
+
antibiogram() function
+- New argument
formatting_type to set any of the 12 options for the formatting of all ‘cells’. This defaults to 10, changing the output of antibiograms to cells with 5% (15/300) instead of the previous standard of just 5.
+- For this reason,
add_total_n is now FALSE at default since the denominators are added to the cells
+- The
ab_transform argument now defaults to "name", displaying antibiotic column names instead of codes
+
+-
antibiotics data set
- Added “clindamycin inducible screening” as
CLI1. Since clindamycin is a lincosamide, the antibiotic selector lincosamides() now contains the argument only_treatable = TRUE (similar to other antibiotic selectors that contain non-treatable drugs)
- Added Amorolfine (
AMO, D01AE16), which is now also part of the antifungals() selector
@@ -141,7 +147,7 @@
- Fixed a bug for when
antibiogram() returns an empty data set
-
Other
+
Other
- Greatly updated and expanded documentation
- Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
diff --git a/pkgdown.yml b/pkgdown.yml
index cd8ef15e..4d5c93b6 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html
-last_built: 2024-09-19T12:44Z
+last_built: 2024-09-22T09:52Z
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 1c29fdb8..385e2f33 100644
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@@ -7,7 +7,7 @@
AMR (for R)
-
2.1.1.9077
+
2.1.1.9078