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(v3.0.1.9027) Fixes #252 and add documentation update regarding #253

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dr. M.S. (Matthijs) Berends
2026-03-06 13:10:33 +01:00
parent 60e8f2bae6
commit c0a394008e
7 changed files with 20 additions and 11 deletions
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man/mo_property.Rd
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@@ -155,7 +155,9 @@ mo_property(x, property = "fullname", language = get_AMR_locale(),
\item{language}{Language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}).}
\item{keep_synonyms}{A \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
\item{keep_synonyms}{A \link{logical} to indicate if outdated, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. Do note that the term "synonym" is in this case jargon from the field of microbial taxonomy - it is not in place to denote that e.g. "Streptococcus Group A" is a synonym of \emph{S. pyogenes}. Though this is practically the case, taxonomically it is not as "Streptococcus Group A" is not even a valid taxonomic name.
The default is \code{FALSE}, which will return a note if outdated taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
\item{...}{Other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'.}