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improve top_n_microorganisms(): add property_for_each, fix property=NULL, enforce rank order (#297)

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Matthijs Berends
2026-06-26 21:40:11 +02:00
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parent 02bd9a71c1
commit f7d353361c
15 changed files with 143 additions and 95 deletions
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NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9076
# AMR 3.0.1.9077
Planned as v3.1.0, end of June 2026.
@@ -37,6 +37,7 @@ Planned as v3.1.0, end of June 2026.
* Fixed some EUCAST Expert Rules, mostly on *S. pneumoniae*
### 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
* `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