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new eucast breakpoints parsing

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Matthijs Berends
2026-08-20 13:28:21 +01:00
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NEWS.md
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# AMR 3.0.1.9086
# AMR 3.0.1.9087
Planned as v3.1.0, end of June 2026.
Planned as v3.1.0, end of September 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.
| `mo_kingdom()` < 3.1.0 | `mo_kingdom()` now | `mo_domain()` (unchanged) |
|------------------------|---------------------|---------------------------|
| Bacteria | Bacillati | Bacteria |
| | Fusobacteriati | Bacteria |
| | Pseudomonadati | Bacteria |
| | Thermotogati | Bacteria |
| | | |
| Archaea | Methanobacteriati | Archaea |
| | Nanobdellati | Archaea |
| | Promethearchaeati | Archaea |
| | Thermoproteati | Archaea |
| | | |
| 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`.
### New