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2026-04-21 20:03:58 +00:00
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reference/top_n_microorganisms.md
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@@ -29,13 +29,13 @@ 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: .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
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.