-
AMR 2.1.1.9031
+
AMR 2.1.1.9032
(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!)
-
A New Milestone: One Health Support (= Human + Veterinary + Environmental)
+
A New Milestone: 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.
@@ -187,8 +187,9 @@
- Function
mo_group_members()
to retrieve the member microorganisms. For example, mo_group_members("Strep group C")
returns a vector of all microorganisms that are in that group.
-
Changed
-
- For MICs:
+
Changed
+- For SIR interpretation, it is now possible to use column names for argument
ab
and mo
: as.sir(..., ab = "column1", mo = "column2")
. This greatly improves the flexibility for users.
+- For MICs:
- Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
- Added new argument
keep_operators
to as.mic()
. This can be "all"
(default), "none"
, or "edges"
. This argument is also available in the new limit_mic_range()
and scale_*_mic()
functions.
- Comparisons of MIC values are now more strict. For example,
>32
is higher than (and never equal to) 32
. Thus, as.mic(">32") == as.mic(32)
now returns FALSE
, and as.mic(">32") > as.mic(32)
now returns TRUE
.
@@ -205,7 +206,7 @@
- Improved overall algorithm of
as.ab()
for better performance and accuracy
-
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 0f305fc4..757cbbfa 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: 2024-05-20T17:01Z
+last_built: 2024-05-20T19:32Z
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 811f2511..77261b4c 100644
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@@ -10,7 +10,7 @@