-
AMR 2.1.1.9033
+
AMR 2.1.1.9034
(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.
@@ -187,12 +187,13 @@
- Function
mo_group_members() to retrieve the member microorganisms of a microorganism group. For example, mo_group_members("Strep group C") returns a vector of all microorganisms that are in that group.
-
Changed
+
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 rescale_mic() 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.
+- Sorting of MIC values (using
sort()) was fixed in the same manner; <0.001 now gets sorted before 0.001, and >0.001 gets sorted after 0.001.
- Updated
italicise_taxonomy() to support HTML output
-
@@ -206,7 +207,7 @@
- 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