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Revamp beta NEWS.md section: concise, user-focused, telegram style (#284)

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* Revamp beta NEWS.md section: concise, user-focused, telegram style

https://claude.ai/code/session_01CnwgKsQqnKNdSD2KjwFAdH

* Loosen NEWS.md telegram style: add context words for clarity

https://claude.ai/code/session_01CnwgKsQqnKNdSD2KjwFAdH

* Add issue/PR references to beta NEWS.md entries

https://claude.ai/code/session_01CnwgKsQqnKNdSD2KjwFAdH

* Add antimicrobial codes to new antimicrobials list in NEWS.md

https://claude.ai/code/session_01CnwgKsQqnKNdSD2KjwFAdH

* Replace em dashes with natural English punctuation in NEWS.md

https://claude.ai/code/session_01CnwgKsQqnKNdSD2KjwFAdH

---------

Co-authored-by: Claude <noreply@anthropic.com>
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2026-05-02 10:31:33 +01:00
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# AMR 3.0.1.9056
This will become release v3.1.0, intended for launch end of May.
Planned as v3.1.0, May 2026.
### New
* Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.
* Support for the [`future`](https://future.futureverse.org) package and its framework, as the previous implementation of parallel computing was slow
- **Breaking change**: `as.sir()` with `parallel = TRUE` now requires a non-sequential `future::plan()` to be active before the call — e.g., `future::plan(future::multisession)` — and throws an informative error if none is set.
- New all-core usage setup: when the number of AB columns is smaller than the number of available cores, rows are now split into batches so all cores stay active (row-batch mode). Previously, a 6-column dataset on a 16-core machine would only use 6 cores; now all 16 are used, with each worker processing a smaller row slice (lower per-worker memory pressure and processing time)
- `antibiogram()` and `wisca()` gained a `parallel` argument using the same `future`/`future.apply` pattern: for WISCA, Monte Carlo simulations are split into `(group, chunk)` job pairs distributed across workers; for grouped antibiograms, each group is processed by a separate worker (#281)
* Integration with the *tidymodels* framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
- `step_mic_log2()` to transform `<mic>` columns with log2, and `step_sir_numeric()` to convert `<sir>` columns to numeric
- New `tidyselect` helpers:
- `all_sir()`, `all_sir_predictors()`
- `all_mic()`, `all_mic_predictors()`
- `all_disk()`, `all_disk_predictors()`
* Data set `esbl_isolates` to practise with AMR modelling
* AMR selectors `ionophores()`, `peptides()`, `phosphonics()` and `spiropyrimidinetriones()`
* Support for Wildtype (WT) / Non-wildtype (NWT) in `as.sir()`, all plotting functions, and all susceptibility/resistance functions.
- `as.sir()` gained an argument `as_wt_nwt`, which defaults to `TRUE` only when `breakpoint_type = "ECOFF"` (#254)
- This transforms the output from S/R to WT/NWT
- Functions such as `susceptibility()` count WT as S and NWT as R
* Function `interpretive_rules()`, which allows future implementation of CLSI interpretive rules (#235)
- `eucast_rules()` has become a wrapper around that function
- Gained argument `add_if_missing` (default: `TRUE`). When set to `FALSE`, rules are only applied to cells that already contain an SIR value; `NA` cells are left untouched. This is useful with `overwrite = TRUE` to update reported results without imputing values for drugs that were not tested (#259)
* Function `amr_course()`, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use
* Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R's `NA_character_` and `NA_integer_`, for use in pipelines that require typed missing values
* EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the `clinical_breakpoints` data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations
* Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting `breakpoint_type = "ECOFF"` in `as.sir()`; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (#254)
* Faster parallel computing via the `future` package; **breaking change**: a non-sequential plan (e.g. `future::plan(future::multisession)`) must be active before using `parallel = TRUE`; `antibiogram()` and `wisca()` now also support `parallel = TRUE` (#281)
* *tidymodels* integration for using SIR, MIC and disk data in modelling pipelines: `step_mic_log2()`, `step_sir_numeric()`, and new column selectors `all_sir()`, `all_mic()`, `all_disk()`
* New `esbl_isolates` data set for practising AMR modelling
* New antimicrobial selectors: `ionophores()`, `peptides()`, `phosphonics()`, `spiropyrimidinetriones()`
* New `interpretive_rules()`, a unified function for EUCAST and CLSI interpretive rules; `eucast_rules()` is now a wrapper around it (#235, #259)
* New `amr_course()` to download and unpack course or webinar materials from GitHub in one call
* Typed missing value constants `NA_ab_` and `NA_mo_`, for use in pipelines that need missing values of a specific class
### Fixes
* Fixed a bug in `as.sir()` where values that were purely numeric (e.g., `"1"`) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter
* Fixed a bug in `as.mic()` where MIC values in scientific notation (e.g., `"1e-3"`) were incorrectly handled because the letter `e` was removed along with other Unicode letters; scientific notation `e` is now preserved
* Fixed a bug in `as.ab()` where certain AB codes containing "PH" or "TH" (such as `ETH`, `MTH`, `PHE`, `PHN`, `STH`, `THA`, `THI1`) would incorrectly return `NA` when combined in a vector with any untranslatable value (#245)
* Fixed a bug in `antibiogram()` for when no antimicrobials are set
* Fixed a bug in `as.sir()` where for numeric input the arguments `S`, `I`, and `R` would not be considered (#244)
* Fixed a bug in plotting MIC values when `keep_operators = "all"`
* Fixed some foreign translations of antimicrobial drugs
* Fixed a bug for printing column names to the console when using `mutate_at(vars(...), as.mic)` (#249)
* Fixed a bug to disregard `NI` for susceptibility proportion functions
* Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (#256)
* Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)
* Fixed translation of foreign languages in `sir_df()` (#272)
* Fixed BRMO classification by including bacterial complexes (#275)
* Fixed `as.sir()` for data frames silently deleting columns whose AB class was already `<sir>` when called a second time (re-running on already-converted data) (#278)
* Fixed `as.sir()` for data frames incorrectly treating metadata columns (e.g. `patient`, `ward`) as antibiotic columns when their names coincidentally matched an antibiotic code; column content is now validated against AMR data patterns before inclusion
* Fixed `as.sir()` ignoring `info = FALSE` for columns with no breakpoints (e.g. cefoxitin against *E. coli*)
* `as.sir()` on data frames: already-converted SIR columns no longer dropped on re-run (#278); metadata columns (e.g. `patient`, `ward`) no longer misidentified as antibiotic columns; `info = FALSE` now suppresses all messages, including for columns without breakpoints
* `as.mic()`: values in scientific notation (e.g. `1e-3`) now handled correctly
* `as.ab()`: codes containing "PH" or "TH" (e.g. `ETH`, `PHE`) no longer return `NA` when mixed with unrecognised input (#245)
* Combined MIC/SIR input values (e.g. `"<= 0.002; S"` or `"S; 0.002"`) now parsed correctly (#252)
* BRMO classification now includes bacterial complexes (#275)
* Translation fixes for Italian CoNS/CoPS names (#256), Dutch antimicrobials, and `sir_df()` foreign-language output (#272)
### Updates
* Renamed `custom_eucast_rules()` to `custom_interpretive_rules()`; old function is now a deprecated wrapper. Renamed `data-raw/eucast_rules.tsv` to `interpretive_rules.tsv` and added `rule.provider` column for multi-guideline (EUCAST/CLSI) support. `clsi_rules()` no longer throws an error (#268)
* `as.sir()` with `reference_data`: custom guideline names now correctly classify values as R using EUCAST convention (`> breakpoint_R` for MIC, `< breakpoint_R` for disk); custom breakpoints with `host = NA` now serve as a host-agnostic fallback when no host-specific row matches (#239)
* 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.
* Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
* `as.mic()` and `rescale_mic()` gained the argument `round_to_next_log2`, which can be set to `TRUE` to round all values up to the nearest next log2 level (#255)
* `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
* `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246)
* Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244)
* Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243)
* Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"`
* Interpretation of capped MIC values now consistently returns `"NI"` (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode
* This results in more reliable behaviour compared to previous versions for capped MIC values
* Removed the `"inverse"` option, which has now become redundant
* `ab_group()` now returns values consist with the AMR selectors (#246)
* `custom_eucast_rules()` renamed to `custom_interpretive_rules()`; old name deprecated but still works (#268)
* `mdro()` can now infer resistance from a drug+inhibitor combination when the base drug column is absent (e.g. piperacillin inferred from piperacillin/tazobactam); controlled via new `infer_from_combinations` argument (default `TRUE`) (#209)
* `susceptibility()` / `resistance()`: new `guideline` argument (default EUCAST) to ensure the 'I' category is interpreted correctly per guideline
* Capped MIC handling in `as.sir()` reworked into four clearly defined options: `"none"`, `"conservative"` (new default), `"standard"`, `"lenient"` (#243)
* `as.mic()` / `rescale_mic()`: new `round_to_next_log2` argument to round values up to the nearest log2 dilution level (#255)
* `antimicrobials$group` now a `list`, so drugs belonging to multiple groups are fully represented; use `ab_group(all_groups = TRUE)` to retrieve all groups for a drug (#246)
* New antimicrobials added: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), zorbamycin (`ZOR`)
* Improved console messages with clickable links throughout, powered by `cli` (#191, #265)
# AMR 3.0.1