-
AMR 2.1.1.9053
-
(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!)
+
AMR 2.1.1.9054
+
(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: 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.
@@ -180,15 +180,15 @@
-
ab_url() now supports retrieving the WHOCC url of their ATCvet pages
+- EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 clinical breakpoints to the
clinical_breakpoints data set for usage in as.sir(). EUCAST 2024 (v14.0) is now the new default guideline for all MIC and disks diffusion interpretations.
-
as.sir() now brings additional factor levels: “NI” for non-interpretable and “SDD” for susceptible dose-dependent. Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI. Also, to get quantitative values, as.double() or 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.
- The function group
scale_*_mic(), namely: scale_x_mic(), scale_y_mic(), scale_colour_mic() and scale_fill_mic(). They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
- Function
rescale_mic(), which allows to rescale MIC values to a manually set range. This is the powerhouse behind the scale_*_mic() functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
- 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.
-- Clinical breakpoints and intrinsic resistance of EUCAST 2024 and CLSI 2024 have been added to the
clinical_breakpoints data set for usage in as.sir(). EUCAST 2024 (v14.0) is now the new default guideline for all MIC and disks diffusion interpretations.
-
Changed
+
Changed
- For 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.
- Extended the antibiotic selectors with
nitrofurans() and rifamycins()
@@ -221,7 +221,7 @@
- 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