c500fdb645
R/sir.R (line 571):
Guard purely numeric strings (e.g. "1", "8") from the Unicode letter
filter. Values matching the broad SIR regex but consisting only of digits
must not be stripped; add `x %unlike% "^[0-9+]$"` predicate.
R/mic.R (lines 220-222):
Preserve the letter 'e' during Unicode-letter removal so that MIC values
in scientific notation (e.g. "1e-3", "2.5e-2") survive the cleaning step.
- Line 220: [\\p{L}] → [^e\\P{L}] (remove all letters except 'e')
- Line 222: [^0-9.><= -]+ → [^0-9e.><= -]+ (allow 'e' in whitelist)
tests/testthat/test-mdro.R:
New tests for the drug+inhibitor inference added in the previous commit
(issue #209):
- TZP=R with no PIP column → PIP inferred R → MDRO class elevated
- TZP=S with no PIP column → proxy col is NA (not S) → class lower
- verbose mode emits "Inferring resistance" message
- AMC=R with no AMX column runs without error (Enterococcus faecium)
https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG
The AMR Package for R
Please visit our comprehensive package website https://amr-for-r.org to read more about this package, including many examples and tutorials.
Overview:
- Provides an all-in-one solution for antimicrobial resistance (AMR) data analysis in a One Health approach
- Peer-reviewed, used in over 175 countries, available in 28 languages
- Generates antibiograms - traditional, combined, syndromic, and even WISCA
- Provides the full microbiological taxonomy of ~79 000 distinct species and extensive info of ~620 antimicrobial drugs
- Applies CLSI 2011-2025 and EUCAST 2011-2025 clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation
- Corrects for duplicate isolates, calculates and predicts AMR per antimicrobial class
- Integrates with WHONET, ATC, EARS-Net, PubChem, LOINC, SNOMED CT, and NCBI
- 100% free of costs and dependencies, highly suitable for places with limited resources
The AMR package is a peer-reviewed, free and open-source R package
with zero dependencies to simplify the analysis and prediction of
Antimicrobial Resistance (AMR) and to work with microbial and
antimicrobial data and properties, by using evidence-based methods.
Our aim is to provide a standard for clean and reproducible AMR data
analysis, that can therefore empower epidemiological analyses to
continuously enable surveillance and treatment evaluation in any
setting.
The AMR package supports and can read any data format, including
WHONET data. This package works on Windows, macOS and Linux with all
versions of R since R-3.0 (April 2013). It was designed to work in any
setting, including those with very limited resources. It was created
for both routine data analysis and academic research at the Faculty of
Medical Sciences of the University of Groningen
and the University Medical Center Groningen.
How to get this package
To install the latest ‘release’ version from CRAN:
install.packages("AMR")
To install the latest ‘beta’ version:
install.packages("AMR", repos = "beta.amr-for-r.org")
If this does not work, try to install directly from GitHub using the
remotes package:
remotes::install_github("msberends/AMR")
This AMR package for R is free, open-source software and licensed under the GNU General Public License v2.0 (GPL-2). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.