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2026-04-02 09:54:05 +00:00
parent d6c59896e9
commit d0fd6aa2cc
103 changed files with 293 additions and 265 deletions
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19
reference/top_n_microorganisms.md
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@@ -29,15 +29,16 @@ top_n_microorganisms(x, n, property = "species", n_for_each = NULL,
A character string indicating the microorganism property to use for
filtering. Must be one of the column names of the
[microorganisms](https://amr-for-r.org/reference/microorganisms.md)
data set: "mo", "fullname", "status", "kingdom", "phylum", "class",
"order", "family", "genus", "species", "subspecies", "rank", "ref",
"oxygen_tolerance", "source", "lpsn", "lpsn_parent",
"lpsn_renamed_to", "mycobank", "mycobank_parent",
"mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to",
"prevalence", or "snomed". If `NULL`, the raw values from `col_mo`
will be used without transformation. When using `"species"` (default)
or `"subpecies"`, the genus will be added to make sure each
(sub)species still belongs to the right genus.
data set: .val mo, .val fullname, .val status, .val kingdom, .val
phylum, .val class, .val order, .val family, .val genus, .val species,
.val subspecies, .val rank, .val ref, .val oxygen_tolerance, .val
source, .val lpsn, .val lpsn_parent, .val lpsn_renamed_to, .val
mycobank, .val mycobank_parent, .val mycobank_renamed_to, .val gbif,
.val gbif_parent, .val gbif_renamed_to, .val prevalence, or .val
snomed. If `NULL`, the raw values from `col_mo` will be used without
transformation. When using `"species"` (default) or `"subpecies"`, the
genus will be added to make sure each (sub)species still belongs to
the right genus.
- n_for_each: