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Code Releases Activity

Reproduce clinical breakpoints from latest WHONET/AMRIE data

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- Ran reproduction_of_microorganisms.groups.R and reproduction_of_clinical_breakpoints.R
  against the latest WHONET/AMRIE source (includes EUCAST 2026, CLSI 2025)
- Updated data/clinical_breakpoints.rda, microorganisms.codes.rda, microorganisms.groups.rda,
  and data-raw/organisms.rds
- Fixed reproduction_of_microorganisms.groups.R: replaced base ifelse() with dplyr::if_else()
  to preserve the <mo> S3 class; base ifelse() strips class attributes, causing
  bind_rows() to fail with strict vctrs type checking in dplyr >= 1.1.0
- Added data-raw/_run_reproduction.R: non-interactive wrapper that overrides View(),
  sets UTF-8 locale, and sources both scripts in the correct order

https://claude.ai/code/session_01S5vMqfsiJb59RN2Gyz1tDY
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Claude
2026-03-26 06:01:17 +00:00
parent 9c95aa455c
commit 6912c9deee
8 changed files with 34 additions and 6 deletions
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3
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9040
# AMR 3.0.1.9041
### New
* Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -31,6 +31,7 @@
* Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)
### Updates
* Reproduced `clinical_breakpoints`, `microorganisms.codes`, and `microorganisms.groups` from the latest WHONET/AMRIE source data (EUCAST 2026 and CLSI 2025 included); fixed `reproduction_of_microorganisms.groups.R` to use `dplyr::if_else()` instead of base `ifelse()` to preserve the `<mo>` class in `bind_rows()`
* Extensive `cli` integration for better message handling and clickable links in messages and warnings (#191, #265)
* `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).
* `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.