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@@ -152,32 +152,25 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
## Value
- If `verbose` is set to `TRUE`:
A [data.frame](https://rdrr.io/r/base/data.frame.html) containing
columns `row_number`, `microorganism`, `MDRO`, `reason`,
`all_nonsusceptible_columns`, `guideline`
- CMI 2012 paper - function `mdr_cmi2012()` or `mdro()`:
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with
levels `Negative` \< `Multi-drug-resistant (MDR)` \<
`Extensively drug-resistant (XDR)` \< `Pandrug-resistant (PDR)`
- TB guideline - function `mdr_tb()` or `mdro(..., guideline = "TB")`:
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with
levels `Negative` \< `Mono-resistant` \< `Poly-resistant` \<
`Multi-drug-resistant` \< `Extensively drug-resistant`
- German guideline - function `mrgn()` or
`mdro(..., guideline = "MRGN")`:
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with
levels `Negative` \< `3MRGN` \< `4MRGN`
- Everything else, except for custom guidelines:
Ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with
levels `Negative` \< `Positive, unconfirmed` \< `Positive`. The value
`"Positive, unconfirmed"` means that, according to the guideline, it
is not entirely sure if the isolate is multi-drug resistant and this
should be confirmed with additional (e.g. genotypic) tests
\- If \`verbose\` is set to \`TRUE\`:
A \[data.frame\] containing columns \`row_number\`, \`microorganism\`,
\`MDRO\`, \`reason\`, \`all_nonsusceptible_columns\`, \`guideline\` -
CMI 2012 paper - function \[mdr_cmi2012()\] or \[mdro()\]:
Ordered \[factor\] with levels \`Negative\` \< \`Multi-drug-resistant
(MDR)\` \< \`Extensively drug-resistant (XDR)\` \< \`Pandrug-resistant
(PDR)\` - TB guideline - function \[mdr_tb()\] or \[\`mdro(...,
guideline = "TB")\`\]\[mdro()\]:
Ordered \[factor\] with levels \`Negative\` \< \`Mono-resistant\` \<
\`Poly-resistant\` \< \`Multi-drug-resistant\` \< \`Extensively
drug-resistant\` - German guideline - function \[mrgn()\] or
\[\`mdro(..., guideline = "MRGN")\`\]\[mdro()\]:
Ordered \[factor\] with levels \`Negative\` \< \`3MRGN\` \< \`4MRGN\` -
Everything else, except for custom guidelines:
Ordered \[factor\] with levels \`Negative\` \< \`Positive, unconfirmed\`
\< \`Positive\`. The value \`"Positive, unconfirmed"\` means that,
according to the guideline, it is not entirely sure if the isolate is
multi-drug resistant and this should be confirmed with additional (e.g.
genotypic) tests
## Details