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2026-03-07 17:15:05 +00:00
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18
reference/mo_property.md
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@@ -139,11 +139,17 @@ mo_property(x, property = "fullname", language = get_AMR_locale(),
- keep_synonyms:
A [logical](https://rdrr.io/r/base/logical.html) to indicate if old,
previously valid taxonomic names must be preserved and not be
corrected to currently accepted names. The default is `FALSE`, which
will return a note if old taxonomic names were processed. The default
can be set with the package option
A [logical](https://rdrr.io/r/base/logical.html) 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outdated, previously valid taxonomic names must be preserved and not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 *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The default is `FALSE`, which will return a note if outdated taxonomic
names were processed. The default can be set with the package option
[`AMR_keep_synonyms`](https://amr-for-r.org/reference/AMR-options.md),
i.e. `options(AMR_keep_synonyms = TRUE)` or
`options(AMR_keep_synonyms = FALSE)`.
@@ -479,7 +485,7 @@ mo_mycobank("Candida albicans")
mo_mycobank("Candida krusei")
#> [1] "337013"
mo_mycobank("Candida krusei", keep_synonyms = TRUE)
#> Warning: Function `as.mo()` returned one old taxonomic name. Use `as.mo(...,
#> Warning: Function `as.mo()` returned one outdated taxonomic name. Use `as.mo(...,
#> keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic
#> names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning
#> will be shown once per session.