From 239c5a87a8eaf96f8f5f0863accdf7915eb806e3 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Mon, 12 Oct 2026 12:55:27 +0200 Subject: [PATCH] (v3.0.1.9122) NEWS update --- DESCRIPTION | 2 +- NEWS.md | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a54a14cbb..caee9f10d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 3.0.1.9121 +Version: 3.0.1.9122 Date: 2026-10-12 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 31c9950e4..622cdc00c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9121 +# AMR 3.0.1.9122 Planned as v3.1.0, mid October 2026. @@ -37,7 +37,7 @@ Planned as v3.1.0, mid October 2026. * *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`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), zorbamycin (`ZOR`) +* 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 @@ -45,7 +45,6 @@ Planned as v3.1.0, mid October 2026. * 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) -* Sulbactam/durlobactam (`SUD1`) added to the `antimicrobials` data set (#308) * `sir_combine()` to combine SIR results of multiple antimicrobials into one variable for combination therapy, using the same rules as `antibiogram()` (#321) ### Fixed @@ -73,7 +72,7 @@ Planned as v3.1.0, mid October 2026. * 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) -* `get_author_year()` in the microorganism reproduction script 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") +* 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* @@ -88,7 +87,7 @@ Planned as v3.1.0, mid October 2026. * WT, NWT, NS and NI results were handled incorrectly in `count_*()` and `proportion_*()` with multiple antimicrobials (#321) * `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 data.table, and suggested packages available on the machine that built the package were used even if not available to the user +* 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) @@ -113,6 +112,7 @@ Planned as v3.1.0, mid October 2026. * `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) + # AMR 3.0.1 This is a bugfix release following the release of v3.0.0 in June 2025.