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15
reference/custom_eucast_rules.md
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@@ -85,13 +85,14 @@ There is one exception in columns used for the rules: all column names
of the
[microorganisms](https://amr-for-r.org/reference/microorganisms.md) data
set can also be used, but do not have to exist in the data set. These
column names are: "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", and "snomed".
Thus, this next example will work as well, despite the fact that the
`df` data set does not contain a column `genus`:
column names are: `"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"`, and `"snomed"`. Thus, this next
example will work as well, despite the fact that the `df` data set does
not contain a column `genus`:
y <- custom_eucast_rules(
TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",