5 Commits

Include renames

Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	30021a9831	(v3.0.1.9153) Speed up mdro(), as.sir(), wisca() and wisca_plot() and the binding of mo vectors, fix PDR in the CMI 2012 guideline of mdro() being assigned to the wrong rows, and limit the stratified WISCA example to the 5 most common species	2026-10-16 06:08:26 +02:00
dr. M.S. (Matthijs) Berends	1a1a3abed1	(v3.0.1.9132) Make translating around 50 times faster and coercion of unknown input in as.ab() up to 70 times faster with identical results, use DOIs instead of PubMed URLs, shorten an example line, and reword cran-comments.md	2026-10-14 20:17:28 +02:00
dr. M.S. (Matthijs) Berends	04a2f0b3ac	(v3.0.1.9125) Fix translations being translated again (e.g. Ticarcillinee, groupee) and untranslated parts of combination names, and let as.mo() recognise translated names in the set language, cached per language	2026-10-12 22:25:57 +02:00
tori0513	3eeabf542a	Add add_custom_antimicrobial_synonyms() (#307) (#311) ... Adds add_custom_antimicrobial_synonyms() to add local names, such as trade names, to existing antimicrobials, also via the AMR_custom_ab option. Matching is language-independent; as.ab() now returns NA with a warning for input that is not valid UTF-8.	2026-10-10 09:14:07 +02:00
Matthijs BerendsandClaude Opus 5.5	891d248fab	Improve the session caches of as.ab(), as.mo() and all mo_*() functions (#313) (#314) ... - One cache design for as.ab() and as.mo() in R/aa_session_cache.R: lazily built lookup indices (ATC codes, drug synonyms, SNOMED codes) and coercion caches with the same structure (key, input, value), keyed on input plus outcome-relevant settings - Caches are invalidated whenever the lookup tables change (custom antimicrobials or microorganisms, set_mo_source()) - mo_*() functions use a fast path for valid <mo> input and work on unique values only - synonym_mo_to_accepted_mo() is memoised per code - Fix as.mo() cache keys that never matched again, fast_mode results of as.ab() being reused by regular calls, and ab_reset_session() clearing as.mo() uncertainties Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-10-07 14:29:48 +02:00