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25
reference/antibiogram.md
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@@ -132,25 +132,24 @@ knit_print(x, italicise = TRUE,
`"shortname"` (default), `"gramstain"`, or 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. Can also be `NULL` to not transform the input or `NA` to
consider all microorganisms 'unknown'.
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"`.
Can also be `NULL` to not transform the input or `NA` to consider all
microorganisms 'unknown'.
- ab_transform:
A character to transform antimicrobial input - must be one of the
column names of the
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
data set (defaults to `"name"`): .val ab, .val cid, .val name, .val
group, .val atc, .val atc_group1, .val atc_group2, .val abbreviations,
.val synonyms, .val oral_ddd, .val oral_units, .val iv_ddd, .val
iv_units, or .val loinc. Can also be `NULL` to not transform the
input.
data set (defaults to `"name"`): `"ab"`, `"cid"`, `"name"`, `"group"`,
`"atc"`, `"atc_group1"`, `"atc_group2"`, `"abbreviations"`,
`"synonyms"`, `"oral_ddd"`, `"oral_units"`, `"iv_ddd"`, `"iv_units"`,
or `"loinc"`. Can also be `NULL` to not transform the input.
- syndromic_group: