Data sets for download / own use
-06 October 2024
+10 October 2024
Source:vignettes/datasets.Rmd
datasets.Rmd
ab, cid, name, group, a iv_ddd, iv_units, and loinc.
This data set is in R available as antibiotics
, after
you load the AMR
package.
It was last updated on 6 October 2024 20:30:52 UTC. Find more info +
It was last updated on 10 October 2024 14:38:20 UTC. Find more info about the structure of this data set here.
Direct download links:
- Download as original
-R Data Structure (RDS) file (49 kB)
+R Data Structure (RDS) file (44 kB)
- Download as tab-separated
text file (0.1 MB)
- Download as Microsoft
-Excel workbook (82 kB)
+Excel workbook (75 kB)
- Download as Apache
Feather file (0.1 MB)
@@ -505,7 +505,7 @@ Names and Codes)
AMR 2.1.1.9093
+AMR 2.1.1.9094
(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: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)
+A New Milestone: AMR v3.0 with 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’s Atlantic Veterinary College, 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 veterinary breakpoints from CLSI. Usebreakpoint_type = "animal"
and set thehost
argument to a variable that contains animal species names.
@@ -95,7 +95,7 @@
- Function
Changed
+Changed
- SIR interpretation
- It is now possible to use column names for argument
ab
,mo
, anduti
:as.sir(..., ab = "column1", mo = "column2", uti = "column3")
. This greatly improves the flexibility for users. - Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI. @@ -147,14 +147,14 @@
- Improved algorithm of
first_isolate()
when using the phenotype-based method, to prioritise records with the highest availability of SIR values
- It is now possible to use column names for argument
Other
+Other
- Greatly improved
vctrs
integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such asdplyr
’sbind_rows()
,rowwise()
andc_across()
are now supported for e.g. columns of classmic
. Despite this, thisAMR
package is still zero-dependent on any other package, includingdplyr
andvctrs
. - Greatly updated and expanded documentation
- Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
- Stopped support for SAS (
.xpt
) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.
Older Versions
+Older Versions
This changelog only contains changes from AMR v3.0 (October 2024) and later.
- For prior v2 versions, please see our v2 archive.
- For prior v1 versions, please see our v1 archive. diff --git a/pkgdown.yml b/pkgdown.yml index e17781c4..330b0465 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -12,7 +12,7 @@ articles: resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html WHONET: WHONET.html -last_built: 2024-10-06T20:50Z +last_built: 2024-10-10T14:41Z 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 814e8c9d..80afb4a3 100644 --- a/reference/AMR-options.html +++ b/reference/AMR-options.html @@ -7,7 +7,7 @@ AMR (for R) - 2.1.1.9093 + 2.1.1.9094