Data sets for download / own use
-05 April 2024
+07 April 2024
Source:vignettes/datasets.Rmd
datasets.Rmd
AMR 2.1.1.9016
+AMR 2.1.1.9017
(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 theirsir
equivalents over a year ago
New
+New
- One Health implementation
- Function
as.sir()
now has extensive support for animal breakpoints from CLSI. Usebreakpoint_type = "animal"
and set thehost
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.
@@ -184,7 +184,7 @@
- Function
limit_mic_range()
, which allows to limit MIC values to a manually set range. This is the powerhouse behind thescale_*_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
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
toas.mic()
. This can be"all"
(default),"none"
, or"edges"
. This argument is also available in the newlimit_mic_range()
andscale_*_mic()
functions.
@@ -196,7 +196,7 @@
- Updated all antibiotic DDDs from WHOCC
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