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reference/mdro.md
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@@ -145,26 +145,31 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
`all_nonsusceptible_columns`, `guideline`
- CMI 2012 paper - function `mdr_cmi2012()` or `mdro()`:
Ordered [factor](https://rdrr.io/r/base/factor.html) with levels
`Negative` \< `Multi-drug-resistant (MDR)` \<
Ordered
[factor](https://rdatatable.gitlab.io/data.table/reference/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/r/base/factor.html) with levels
`Negative` \< `Mono-resistant` \< `Poly-resistant` \<
Ordered
[factor](https://rdatatable.gitlab.io/data.table/reference/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/r/base/factor.html) with levels
`Negative` \< `3MRGN` \< `4MRGN`
Ordered
[factor](https://rdatatable.gitlab.io/data.table/reference/fctr.html)
with levels `Negative` \< `3MRGN` \< `4MRGN`
- Everything else, except for custom guidelines:
Ordered [factor](https://rdrr.io/r/base/factor.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
Ordered
[factor](https://rdatatable.gitlab.io/data.table/reference/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
## Details