-
AMR 2.1.1.9022
+
AMR 2.1.1.9025
(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.
@@ -185,7 +185,7 @@
- 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
+
Changed
- 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.
@@ -197,9 +197,12 @@
- 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.
- Updated all ATC codes from WHOCC
- Updated all antibiotic DDDs from WHOCC
+- Fix for using a manual value for
mo_transform in antibiogram()
+
+- Fix for mapping ‘high level’ antibiotics in
as.ab() (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
-
Other
+
Other
- Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input