Built site for AMR@3.0.1.9030: e2102c0

reference/as.mo.md

@@ -81,11 +81,17 @@ NA_mo_
 
 - 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+  outdated, previously valid taxonomic names must be preserved and not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+  The default is `FALSE`, which will return a note if outdated taxonomic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)`.
@@ -141,8 +147,8 @@ NA_mo_
 
   A [logical](https://rdrr.io/r/base/logical.html) to indicate that info
   must be printed, e.g. a progress bar when more than 25 items are to be
-  coerced, or a list with old taxonomic names. The default is `TRUE`
-  only in interactive mode.
+  coerced, or a list with outdated taxonomic names. The default is
+  `TRUE` only in interactive mode.
 
 - ...:
 
@@ -230,7 +236,7 @@ There are three helper functions that can be run after using the
 
 - Use `mo_renamed()` to get a
   [data.frame](https://rdrr.io/r/base/data.frame.html) with all values
-  that could be coerced based on old, previously accepted taxonomic
+  that could be coerced based on outdated, previously accepted taxonomic
   names.
 
 ### For Mycologists