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(v3.0.1.9127) update NEWS

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dr. M.S. (Matthijs) Berends committed 2026-10-13 08:44:38 +02:00
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CLAUDE.md
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@@ -165,7 +165,24 @@ Version format: `major.minor.patch.dev` (e.g., `3.0.1.9021`)
- Development versions use a `.9xxx` suffix
- Stable CRAN releases drop the dev suffix (e.g., `3.0.1`)
- `NEWS.md` uses sections **New**, **Fixes**, **Updates** with GitHub issue references (`#NNN`)
- `NEWS.md` follows the style of the v3.0.0 section; see *NEWS.md style* below
### NEWS.md style
Each version section follows the v3.0.0 section of `NEWS.md`:
- After the `# AMR <version>` heading, an optional line on the planned release, then a short intro paragraph summarising the main changes in plain prose
- Sub-headings, in this order and only when they have content: `### Breaking`, `### New`, `### Changed`, `### Other`
- **Breaking**: changes that can alter results or break existing code (renamed or removed arguments, options or values, changed return values, new requirements); explain what changed and how to get the old behaviour
- **New**: new functions, arguments, data sets, columns, selectors, antimicrobials and breakpoints, grouped under bold thematic bullets (e.g. `* **Updated clinical breakpoints**`) with nested bullets beneath; end with a `* **Other**` group for items that fit no theme
- **Changed**: improvements and bug fixes together (there is no separate fixes section), grouped by function or data set as a plain parent bullet (e.g. ``* SIR interpretation (`as.sir()`)``, ``* `microorganisms` data set``) with nested bullets beneath; items that fit no group are single top-level bullets at the end
- **Other**: documentation, vignettes, website, contributors and console output
- Each function or data set gets exactly one group; never scatter entries for the same function (e.g. `as.mo()`) across the section
- Bug fixes start with "Fixed ..." or state the corrected behaviour (e.g. "now returns `NA` with a warning instead of an error")
- Write descriptive, complete sentences, in British English; a single-sentence bullet has no final full stop, a bullet of several sentences ends with one
- Use "e.g.," and "i.e.,", backticks for code, functions with `()`, and italics for taxonomic names
- Add GitHub issue references at the end of the item, as `(#NNN)` or `(#NNN, #NNN)`
- Never use em dashes
### Local commits on `main`: never touch the version number
@@ -201,12 +218,7 @@ echo "$currentversion"
The `+ 1` accounts for the fact that this PR's squash commit is not yet on the default branch. Set **both** of these files to the resulting version string (and only once per PR, even across multiple commits):
1. **`DESCRIPTION`** — the `Version:` field
2. **`NEWS.md`** — **only replace line 1** (the `# AMR <version>` heading) with the new version number; do **not** create a new section. `NEWS.md` is a **continuous log** for the entire current `x.y.z.9nnn` development series: all changes since the last stable release accumulate under that single heading. After updating line 1, append the new change as a bullet under the appropriate sub-heading (`### New`, `### Fixes`, or `### Updates`).
Style rules for `NEWS.md` entries:
- Be **extremely concise** — one short line per item
- Do **not** end with a full stop (period)
- No verbose explanations; just the essential fact
2. **`NEWS.md`** — **only replace line 1** (the `# AMR <version>` heading) with the new version number; do **not** create a new section. `NEWS.md` is a **continuous log** for the entire current `x.y.z.9nnn` development series: all changes since the last stable release accumulate under that single heading. After updating line 1, add the new change to the appropriate sub-heading and group, following *NEWS.md style* above. If the change belongs to an existing group (e.g. `as.mo()`), add it there or amend the existing bullet instead of adding a new top-level bullet.
If `git describe` fails (e.g. no tags exist in the environment), fall back to reading the current version from `DESCRIPTION` and adding 1 to the last numeric component — but only if no bump has already been made in this PR.
DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR
Version: 3.0.1.9126
Date: 2026-10-12
Version: 3.0.1.9127
Date: 2026-10-13
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by
NEWS.md
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@@ -1,9 +1,9 @@
# AMR 3.0.1.9126
# AMR 3.0.1.9127
Planned as v3.1.0, mid October 2026.
### Breaking Changes
* The former *kingdoms* Bacteria and Archaea are now each divided into four kingdoms with new top-level *domains* 'Bacteria' and 'Archaea' (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new `domain` column in the `microorganisms` data set was added, and more importantly, `mo_kingdom()` now returns the formal kingdom (e.g. `"Pseudomonadati"` instead of `"Bacteria"`). Use `mo_domain()` for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), `kingdom` and `domain` are identical.
### Breaking
* The former *kingdoms* Bacteria and Archaea are now each divided into four kingdoms, with new top-level *domains* Bacteria and Archaea (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new `domain` column was added to the `microorganisms` data set, and `mo_kingdom()` now returns the formal kingdom (e.g., `"Pseudomonadati"` instead of `"Bacteria"`). Use `mo_domain()` for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), `kingdom` and `domain` are identical.
| `mo_kingdom()` < 3.1.0 | `mo_kingdom()` now | `mo_domain()` (unchanged) |
|------------------------|---------------------|---------------------------|
@@ -20,98 +20,116 @@ Planned as v3.1.0, mid October 2026.
| Fungi | Fungi | Fungi |
| | | |
| Protozoa | Protozoa | Protozoa |
Thus, `mo_domain()` was previously an alias of `mo_kingdom()`; it is now a distinct function returning the domain. Output of `mo_domain()` is therefore unchanged, while `mo_kingdom()` now returns the formal, new kingdom.
* Faster parallel computing via the `future` package for `as.sir()` and `wisca()`: a non-sequential plan (e.g. `future::plan(future::multisession)`) must be active before using `parallel = TRUE`.
* `as.mo()` no longer guesses unknown MO codes (these become `NA` with a warning), and MO codes from versions before v2.0.0 are no longer supported
Previously, `mo_domain()` was an alias of `mo_kingdom()`; it is now a distinct function. Its output is therefore unchanged, while `mo_kingdom()` now returns the new formal kingdom. A one-time note per session explains this change when bacterial or archaeal records are queried.
* Parallel computing in `as.sir()`, `antibiogram()`, and `wisca()` now uses the `future` and `future.apply` packages, which is faster. A non-sequential plan (e.g., `future::plan(future::multisession)`) must be active before using `parallel = TRUE` (#281).
* The options of `capped_mic_handling` in `as.sir()` have been redefined as `"none"`, `"conservative"`, `"standard"` (default), and `"lenient"`. The option `"inverse"` is no longer available (#243).
### New
* 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
* Human EUCAST breakpoints from 2019 (v9.0) on, are now retrieved directly from EUCAST Excel files instead of relying on the WHONET repository.
* `clinical_breakpoints` now contains blocking rows (`NA` breakpoints, reason in `note`) where EUCAST gives no breakpoint for an organism, so `as.sir()` no longer falls back to the breakpoint of a broader taxon
* Restrictions in EUCAST notes are applied, e.g. zone diameter breakpoints for *E. coli* only
* EUCAST PK-PD (non-species related) breakpoints 2019-2023 and *H. parainfluenzae* MIC breakpoints are included
* 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)
* *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 antimicrobials: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), Sulbactam/durlobactam (`SUD1`, #308), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), zorbamycin (`ZOR`)
* New `interpretive_rules()`, a unified function for EUCAST and CLSI interpretive rules; `eucast_rules()` is now a wrapper around it (#235, #259)
* New `morphology` column in the `microorganisms` data set and corresponding `mo_morphology()` function, returning the cell shape of bacteria. Data sourced from BacDive; values prefixed with "likely" are extrapolated from genus-level consensus. New `add_morphology` argument was added to `mo_gramstain()` to return combined results such as `"Gram-negative rods"`.
* 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
* New `wisca_plot()` to assess the susceptibility and incidence distributions from the Monte Carlo simulations
* A registry of all microbial IDs (MO codes) since v2.0.0 now prevents existing IDs from being reused or mixed up; IDs of earlier releases are translated to the current ID of the same taxon
* `add_custom_antimicrobial_synonyms()` to add local names, such as trade names, to existing antimicrobials (#307)
* `sir_combine()` to combine SIR results of multiple antimicrobials into one variable, for combination therapy (`method = "most_susceptible"`) or resistance within a group (`method = "most_resistant"`) (#321)
* **Updated clinical breakpoints**
* EUCAST 2026 and CLSI 2026 are now supported, by adding over 5,700 new breakpoints to the `clinical_breakpoints` data set. EUCAST 2026 is now the default guideline for all MIC and disk diffusion interpretations.
* Human EUCAST breakpoints from 2019 (v9.0) onwards are now retrieved directly from the EUCAST Excel files, instead of relying on the WHONET repository. As a result:
* `clinical_breakpoints` now contains blocking rows (`NA` breakpoints, with the reason in `note`) where EUCAST gives no breakpoint for an organism, so that `as.sir()` no longer falls back to the breakpoint of a broader taxon
* Restrictions in EUCAST notes are applied, e.g., zone diameter breakpoints for *E. coli* only
* EUCAST PK-PD (non-species related) breakpoints of 2019-2023 and *H. parainfluenzae* MIC breakpoints are now included
* **Wildtype/Non-wildtype interpretation**
* `as.sir()` now returns WT/NWT (Wildtype/Non-wildtype) when using ECOFF-based interpretation with `breakpoint_type = "ECOFF"`. WT/NWT results are fully supported in all resistance and susceptibility functions and in all plots (#254).
* **Unified interpretive rules**
* New function `interpretive_rules()` applies the interpretive rules of both EUCAST and CLSI. `eucast_rules()` is now a wrapper around this function (#235, #259).
* Species named in a rule now also match all other names of the same accepted taxon (e.g., 'Clostridium ramosum' for *Thomasclavelia ramosa*). This also updated the `intrinsic_resistant` data set.
* **Support for `tidymodels` pipelines**
* New recipe steps `step_mic_log2()` and `step_sir_numeric()` to use MIC and SIR data in modelling pipelines
* New column selectors `all_sir()`, `all_mic()`, and `all_disk()`
* New `esbl_isolates` data set for practising AMR modelling
* **Morphology of bacteria**
* New `morphology` column in the `microorganisms` data set, with the corresponding function `mo_morphology()` to return the cell shape of bacteria. Data are sourced from BacDive; values prefixed with "likely" are extrapolated from the consensus at genus level.
* New argument `add_morphology` in `mo_gramstain()` to return combined results, such as `"Gram-negative rods"`
* **Antimicrobials**
* New function `sir_combine()` to combine SIR results of multiple antimicrobials into one variable, for combination therapy (`method = "most_susceptible"`) or for resistance within a group (`method = "most_resistant"`) (#321)
* New function `add_custom_antimicrobial_synonyms()` to add local names, such as trade names, to existing antimicrobials (#307)
* New antimicrobial selectors `ionophores()`, `peptides()`, `phosphonics()`, and `spiropyrimidinetriones()`
* New antimicrobials: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), sulbactam/durlobactam (`SUD1`, #308), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
* **Other**
* New function `wisca_plot()` to assess the distributions of susceptibility and incidence from the Monte Carlo simulations of WISCA
* New function `amr_course()` to download and unpack course or webinar materials from GitHub in one call
* New typed missing value constants `NA_ab_` and `NA_mo_`, for use in pipelines that need missing values of a specific class
* A registry of all MO codes since v2.0.0 now prevents existing codes from being reused or mixed up. Codes of earlier releases are translated to the current code of the same taxon.
### Fixed
* `as.mo()` returned *Salmonella bongori* or another subspecies for *Salmonella* serovars written with the species, such as "Salmonella enterica serovar Typhi"
* EUCAST breakpoint rules for *Aerococcus* (v12 onwards) were never applied, and *Pasteurella* rules were partly filed under *Neisseria meningitidis* (#290)
* Streptomycin breakpoints imported from WHONET were coded as streptoduocin (`STR`) instead of streptomycin (`STR1`)
* CLSI breakpoints for sulbactam/durlobactam were coded as sulfadimethoxine (`SUD`), and EUCAST 2011 breakpoints for roxithromycin were missing (#308)
* Setting `options(AMR_guideline = "EUCAST 2012")` or any year-qualified value no longer causes errors or silent wrong behaviour in `interpretive_rules()`, `resistance()`, `susceptibility()`, `count_resistant()`, `count_susceptible()`, and SIR plotting/printing functions (#298)
* `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
* Assumption of disk zones are now preferred over MIC values when input is only whole numbers (#291)
* Capped MICs (e.g. `<=0.5`) are now `I` instead of `S` or `NI` if there is no S category, i.e. an off-scale S breakpoint such as EUCAST's 0.001 mg/L (#295)
### Changed
* SIR interpretation (`as.sir()`)
* New argument `enforce_method` (`"auto"`, `"mic"`, or `"disk"`) to force the interpretation method when S3 class information is lost, e.g., when called from Python (#291)
* When input consists of whole numbers only, disk zones are now assumed rather than MIC values (#291)
* Capped MICs (e.g., `<=0.5`) now return `I` instead of `S` or `NI` if there is no S category, i.e., in case of an off-scale S breakpoint such as EUCAST's 0.001 mg/L (#295)
* Capped MICs are no longer forced to `S` or `R` if there is no breakpoint for the drug-bug combination
* Documented default of `capped_mic_handling` corrected to `"standard"`
* `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)
* `as.ab()`: results of `fast_mode` (used internally) were remembered and reused by later regular calls, which could return `NA` for valid input (#313)
* `as.ab()`: input that is not valid UTF-8 (e.g. text exported in a local encoding such as CP949) now returns `NA` with a warning instead of an error
* `as.mo()`: previously coerced input was often not recognised again, e.g. for an unknown species of a known genus, so it was matched again on every call (#313)
* `ab_reset_session()` no longer clears the uncertainties of `as.mo()` (#313)
* Combined MIC/SIR input values (e.g. `"<= 0.002; S"` or `"S; 0.002"`) now parsed correctly (#252)
* `as.mo()`:
* Input of the form `"X complex"` now falls back to `"X"` when the complex is not a distinct taxon in the database, preventing `NA` results for valid clinical descriptions such as `"Proteus vulgaris complex"` (#287)
* Abbreviated-genus input (e.g. `"S. apiospermum"`) now correctly ranks candidates whose species epithet exactly matches the input above more-prevalent organisms whose species does not match; fixes `"S. apiospermum"` resolving to *Staphylococcus* instead of *Scedosporium apiospermum* (#288)
* Abbreviated-genus input for species that have subspecies (e.g. `"P. ovale"`) now collapses to the species-rank record instead of incorrectly matching a more-prevalent organism; explicit subspecies queries (e.g. `"P. ovale curtisi"`) are preserved (#288)
* Author references in the `microorganisms` dataset now strips `emend.` and everything after it, so `ref` reflects the combination authority rather than the emendation author (e.g. *Rhodococcus equi* now returns "Goodfellow et al., 1977" instead of "Nouioui et al., 2018")
* BRMO classification now includes bacterial complexes (#275)
* Translation fixes for Italian CoNS/CoPS names (#256), Dutch antimicrobials, and `sir_df()` foreign-language output (#272)
* Fixed some EUCAST Expert Rules, mostly on *S. pneumoniae*
* Logical comparison (`==`, `!=`) of `sir` class with a `factor` is now possible on R >= 4.3
* `mo_current()` and `as.mo()` could not find the current name of some synonyms with multiple sources (e.g. *Chaetomium abuense*)
* `interpretive_rules()`: species named in a rule now also match all other names of the same accepted taxon (e.g. 'Clostridium ramosum' for *Thomasclavelia ramosa*), which also updates `intrinsic_resistant`
* *Erysipelatoclostridium* and its species are now synonyms of *Thomasclavelia*; *E. merdavium* is retired
* Taxonomy: names that a source lists twice now take the correct record (e.g. *Eggerthella lenta*, *Gordonia amarae* and *Anisakis simplex* were synonyms without a current name)
* Taxonomy: synonyms without a current name are linked via LPSN or removed, with their codes retired; the *M. tuberculosis* complex is always kept
* Taxonomy: consistent higher taxonomy and parent records, and data sets refer only to current names (except `intrinsic_resistant`)
* `antimicrobials`: trade names of combinations (Tazocin, Timentin, Recarbrio, Exblifep) were listed under a single component, and names of screening libraries and suppliers (e.g. Prestwick, Spectrum) as synonyms (#315)
* WT, NWT, NS and NI results were handled incorrectly in `count_*()` and `proportion_*()` with multiple antimicrobials (#321)
* Translations were translated again, e.g. "Ticarcillinee" in Dutch and "groupee" in French, and parts of combination names were left untranslated
* `as.mo()` now recognises translated names in the set language, such as the output of `mo_name(x, language = "fr")`
* `g.test()` returned the degrees of freedom as `argument` instead of `parameter`, so they were not printed
* `antibiogram()` and `wisca()` failed without the `antimicrobials` argument if tidyselect was not available, e.g. for binary installations without dplyr
* R could crash after unloading the `data.table` package, and suggested packages available on the machine that built the package were used even if not available to the user
### Updated
* Faster `as.ab()`, `as.mo()` and all `mo_*()` functions through one consistent session cache design, which is cleared when lookup tables change, e.g. after `add_custom_microorganisms()` (#313)
* `mo_*()` functions retrieve properties of valid `<mo>` input directly, and only for unique values
* The mapping of outdated taxonomic names to their current names is remembered per code
* Fixed the documented default of `capped_mic_handling`, which is `"standard"`
* On data frames, already-converted SIR columns are no longer dropped on a re-run (#278)
* Metadata columns (e.g., `patient`, `ward`) are no longer misidentified as antimicrobial columns
* `info = FALSE` now suppresses all messages, including those for columns without breakpoints
* Combined MIC/SIR input values (e.g., `"<= 0.002; S"` or `"S; 0.002"`) are now parsed correctly (#252)
* Setting a year-qualified guideline, such as `options(AMR_guideline = "EUCAST 2012")`, no longer causes errors or silently wrong results in `interpretive_rules()`, `resistance()`, `susceptibility()`, `count_resistant()`, `count_susceptible()`, and the SIR plotting and printing functions (#298)
* `clinical_breakpoints` data set
* Fixed EUCAST breakpoint rules for *Aerococcus* (v12 onwards), which were never applied, and for *Pasteurella*, which were partly filed under *Neisseria meningitidis* (#290)
* Fixed streptomycin breakpoints imported from WHONET, which were coded as streptoduocin (`STR`) instead of streptomycin (`STR1`)
* Fixed CLSI breakpoints for sulbactam/durlobactam, which were coded as sulfadimethoxine (`SUD`), and added the missing EUCAST 2011 breakpoints for roxithromycin (#308)
* Fixed some EUCAST Expert Rules, mostly on *S. pneumoniae*
* Microorganism coercion (`as.mo()`) and properties (`mo_*()`)
* Considerably faster through one consistent session cache design, which is cleared when lookup tables change, e.g., after `add_custom_microorganisms()` (#313)
* `mo_*()` functions now retrieve properties of valid `mo` input directly, and only for unique values
* The mapping of outdated taxonomic names to their current names is now remembered per code
* Previously coerced input is now recognised again, e.g., for an unknown species of a known genus, instead of being matched again on every call (#313)
* `mo_uncertainties()` now also lists uncertainties of previously coerced input
* `top_n_microorganisms()`: new `property_for_each` argument for sub-grouping within top *n* groups; rank ordering enforced (only lower taxonomic ranks allowed); fixed `property = NULL` not being accepted; inner filter now tracks original row indices to prevent cross-group contamination
* Taxonomic update for all microorganisms, now updated to COL 2026-04-18 XR, LPSN and BacDive of October 2026, and MycoBank of January 2026
* `mo_kingdom()` now returns the formal taxonomic kingdom; a one-time note per session explains the change when querying bacterial or archaeal records.
* `mo_taxonomy()` and `mo_info()` gained `domain` for the list output
* `antibiogram()` and `wisca()` now also support parallel computing via the argument `parallel = TRUE` (#281)
* `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)
* `wisca()` now more strictly follows Bielicki et al. (2016) by using $\text{Beta}(1, 9999)$ for intrinsically resistant pairs, forcing near-zero susceptibility regardless of observed data (based on EUCAST Expected Resistant Phenotypes)
* `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` is now a `list`, so that drugs belonging to multiple groups are fully represented; use `ab_group(all_groups = TRUE)` to retrieve all groups for a drug (#246)
* Improved console messages with clickable links throughout, powered by `cli` if it is installed (#191, #265)
* `as.disk()`: input validation is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter
* `as.sir()` gains an `enforce_method` argument (`"auto"`, `"mic"`, or `"disk"`) to force the interpretation method when S3 class information is lost, e.g. when called from Python (#291)
* `AMR for Python` vignette: added sections on installation channels (stable CRAN vs. development GitHub via `AMR.beta`) and on using `enforce_method` in `as_sir()` from Python
* Improved French translations, kindly provided by Mathilde Garé (#322)
* Translated names in the set language are now recognised, such as the output of `mo_name(x, language = "fr")`, and cached per language
* Input of the form `"X complex"` now falls back to `"X"` when the complex is not a distinct taxon, preventing `NA` for valid clinical descriptions such as `"Proteus vulgaris complex"` (#287)
* Abbreviated genus input now ranks candidates with an exactly matching species epithet above more prevalent organisms, so that e.g. `"S. apiospermum"` returns *Scedosporium apiospermum* instead of a *Staphylococcus* species (#288)
* Abbreviated genus input for species with subspecies (e.g., `"P. ovale"`) now returns the species instead of a more prevalent organism, while explicit subspecies (e.g., `"P. ovale curtisi"`) are preserved (#288)
* *Salmonella* serovars written with the species, such as `"Salmonella enterica serovar Typhi"`, no longer return *Salmonella bongori* or another subspecies
* `as.mo()` and `mo_current()` now find the current name of synonyms with multiple sources (e.g., *Chaetomium abuense*)
* `mo_taxonomy()` and `mo_info()` now contain an extra element `domain`
* `microorganisms` data set
* Taxonomic update of all microorganisms, now based on COL 2026-04-18 XR, LPSN and BacDive of October 2026, and MycoBank of January 2026
* Names listed twice by a source now take the correct record (e.g., *Eggerthella lenta*, *Gordonia amarae*, and *Anisakis simplex* were synonyms without a current name)
* Synonyms without a current name are now linked via LPSN or removed, with their codes retired. The *M. tuberculosis* complex is always kept.
* Higher taxonomy and parent records are now consistent, and all data sets refer only to current names (except `intrinsic_resistant`)
* *Erysipelatoclostridium* and its species are now synonyms of *Thomasclavelia*; *E. merdavium* is retired
* Author references now strip `emend.` and everything after it, so that `ref` reflects the combination authority rather than the emendation author (e.g., *Rhodococcus equi* now returns "Goodfellow et al., 1977" instead of "Nouioui et al., 2018")
* Antimicrobial coercion (`as.ab()`) and `antimicrobials` data set
* Considerably faster through the same session cache design as `as.mo()` (#313)
* Fixed a bug where results of `fast_mode` (used internally) were remembered and reused by later regular calls, which could return `NA` for valid input (#313)
* Codes containing "PH" or "TH" (e.g., `ETH`, `PHE`) no longer return `NA` when mixed with unrecognised input (#245)
* Input that is not valid UTF-8 (e.g., text exported in a local encoding such as CP949) now returns `NA` with a warning instead of an error
* `ab_reset_session()` no longer clears the uncertainties of `as.mo()` (#313)
* `antimicrobials$group` is now a `list`, so that drugs belonging to multiple groups are fully represented. Use `ab_group(all_groups = TRUE)` to retrieve all groups of a drug (#246).
* Trade names of combinations (Tazocin, Timentin, Recarbrio, Exblifep) were listed under a single component, and names of screening libraries and suppliers (e.g., Prestwick, Spectrum) as synonyms. These have been corrected (#315).
* Antibiograms (`antibiogram()` and `wisca()`)
* `wisca()` now follows Bielicki *et al.* (2016) more strictly by using $\text{Beta}(1, 9999)$ for intrinsically resistant pairs, forcing near-zero susceptibility regardless of observed data (based on EUCAST Expected Resistant Phenotypes)
* Fixed a bug where both functions failed without the `antimicrobials` argument if `tidyselect` was not available, e.g., for binary installations without `dplyr`
* Resistance and susceptibility calculation
* New argument `guideline` (default: EUCAST) in `susceptibility()` and `resistance()` to interpret the 'I' category correctly per guideline
* `count_*()` and `proportion_*()` with multiple antimicrobials behave as in AMR 3.0.1 again, and now handle WT, NWT, NS, and NI results correctly (#321)
* MICs and disk diffusion
* New argument `round_to_next_log2` in `as.mic()` and `rescale_mic()` to round values up to the nearest log2 dilution level (#255)
* `as.mic()` now handles values in scientific notation (e.g., `1e-3`) correctly
* Input validation of `as.disk()` is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter
* MDRO determination (`mdro()`)
* Resistance can now be inferred from a drug/inhibitor combination when the column of the base drug is absent (e.g., piperacillin inferred from piperacillin/tazobactam). This is controlled with the new argument `infer_from_combinations` (default: `TRUE`) (#209).
* BRMO classification now includes bacterial complexes (#275)
* `top_n_microorganisms()`
* New argument `property_for_each` for sub-grouping within the top *n* groups. Rank ordering is enforced, so that only lower taxonomic ranks are allowed.
* `property = NULL` is now accepted
* The inner filter now tracks the original row indices, to prevent contamination across groups
* Translations
* Improved French translations, kindly provided by Mathilde Garé (#322)
* Improved translations of combination names and antimicrobial groups in 20 languages
* Translations are no longer translated again (e.g., "Ticarcillinee" in Dutch and "groupee" in French), and parts of combination names are no longer left untranslated
* Fixed Italian names of CoNS and CoPS (#256), Dutch names of antimicrobials, and output of `sir_df()` in other languages (#272)
* `custom_eucast_rules()` has been renamed to `custom_interpretive_rules()`. The old name is now deprecated but still works (#268).
* Logical comparison (`==`, `!=`) of the `sir` class with a `factor` is now possible on R >= 4.3
* Fixed a bug in `g.test()` that returned the degrees of freedom as `argument` instead of `parameter`, so that they were not printed
* Fixed a bug where R could crash after unloading the `data.table` package, and where suggested packages available on the machine that built the package were used even if they were not available to the user
### Other
* Improved console messages with clickable links throughout the package, powered by `cli` if it is installed (#191, #265)
* The 'AMR for Python' vignette now contains sections on installation channels (stable from CRAN, or development from GitHub via `AMR.beta`) and on using `enforce_method` in `as_sir()` from Python
# AMR 3.0.1
@@ -194,7 +212,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
### Changed
* SIR interpretation
* Support for parallel computing to greatly improve speed using the `parallel` package (part of base R). Use `as.sir(your_data, parallel = TRUE)` to run SIR interpretation using multiple cores.
* It is now possible to use column names for arguments `guideline`, `ab`, `mo`, and `uti`: `as.sir(..., ab = "column1", mo = "column2", uti = "column3")`. This greatly improves the flexibility for users.
* For `as.sir()`, it is now possible to use column names for arguments `guideline`, `ab`, `mo`, and `uti`
* Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.
* To get quantitative values, `as.double()` on a `sir` object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become `NA`). Other functions using `sir` classes (e.g., `summary()`) are updated to reflect the change to contain NI and SDD.
* Following CLSI interpretation rules, values outside the log2-dilution range will be rounded upwards to the nearest log2-level before interpretation. Only if using a CLSI guideline.