-
AMR 3.0.1.9079
+
AMR 3.0.1.9080
Planned as v3.1.0, end of June 2026.
-
Breaking Changes
+
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.
- 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.
-
New
+
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
- 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)
-
@@ -74,7 +74,7 @@
- New
wisca_plot() to assess the susceptibility and incidence distributions from the Monte Carlo simulations
-
Fixed
+
Fixed
- 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()
@@ -93,6 +93,7 @@
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)
-
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”)
@@ -102,7 +103,7 @@
-
Updated
+
Updated
-
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 June 2026
diff --git a/news/index.md b/news/index.md
index 5fac2c13f..784d81764 100644
--- a/news/index.md
+++ b/news/index.md
@@ -1,6 +1,6 @@
# Changelog
-## AMR 3.0.1.9079
+## AMR 3.0.1.9080
Planned as v3.1.0, end of June 2026.
@@ -117,6 +117,11 @@ Planned as v3.1.0, end of June 2026.
`"S. apiospermum"` resolving to *Staphylococcus* instead of
*Scedosporium apiospermum*
([\#288](https://github.com/msberends/AMR/issues/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](https://github.com/msberends/AMR/issues/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
diff --git a/pkgdown.yml b/pkgdown.yml
index 120c62ce1..aa29fa035 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
-last_built: 2026-06-27T12:34Z
+last_built: 2026-06-27T13:26Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles
diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html
index a154ba60c..daa00d63c 100644
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -7,7 +7,7 @@
AMR (for R)
- 3.0.1.9079
+ 3.0.1.9080