-
AMR 2.1.1.9060
+
AMR 2.1.1.9061
(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, 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.
@@ -194,7 +194,7 @@
-
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.
@@ -233,7 +233,7 @@
- Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range
-
Other
+
Other
- 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 8ece916a..733e4d57 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: 2024-06-19T13:11Z
+last_built: 2024-06-19T13:44Z
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 5734484c..2ac7c102 100644
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@@ -10,7 +10,7 @@