NEWS

rhinotypeR 2025-10-21 (2025-10-21)

Example and test errors related to internal helpers (compareAndColorSequences(), compute_cache()) now handled safely using \dontrun{} and updated documentation.
Removed outdated License stub issue and corrected DESCRIPTION metadata formatting.
Corrected internal tests referencing deprecated testthat::local_null_device().

CountSNPs() re-implementation: directly computes pairwise SNP counts without relying on model-based rounding (e.g., from MSA2dist). No rounding artifacts

New function: alignToRefs(), which aligns user sequences to the packaged rhinovirus prototype references using msa::msa() (ClustalW, ClustalOmega, or MUSCLE), with an option to trim alignments to the non-gap span of a chosen reference.

SNPeek() and plotAA(): now support zooming to specific genomic regions and highlighting individual sequences of interest.
assignTypes(): now reports the genetic distance to the nearest prototype even when the query is "unassigned".
Distance calculation: switched to using MSA2dist for pairwise distance computation. This provides broader model support — access to all substitution models in ape::dist.dna, in addition to the "IUPAC" model.
Data access: prototype and example datasets are now exported as packaged objects (rhinovirusVP4, rhinovirusPrototypesVP4) instead of being accessed via system.file(), simplifying workflows.
Improved documentation:
- Improved explanations and runnable examples added where feasible.
- Visualization functions return results invisibly to avoid console clutter, while still allowing advanced users to capture outputs.
Code style and formatting improved (e.g.,consistent internal helpers).