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reference/mdro.md

@@ -6,11 +6,24 @@ according to international, national, or custom guidelines.
 ## Usage
 
 ``` r
-mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
-  carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
-  info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
-  verbose = FALSE, only_sir_columns = any(is.sir(x)),
-  infer_from_combinations = TRUE, ...)
+mdro(
+  x = NULL,
+  guideline = "CMI 2012",
+  col_mo = NULL,
+  esbl = NA,
+  carbapenemase = NA,
+  mecA = NA,
+  mecC = NA,
+  vanA = NA,
+  vanB = NA,
+  info = interactive(),
+  pct_required_classes = 0.5,
+  combine_SI = TRUE,
+  verbose = FALSE,
+  only_sir_columns = any(is.sir(x)),
+  infer_from_combinations = TRUE,
+  ...
+)
 
 brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
 
@@ -18,11 +31,14 @@ mrgn(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
 
 mdr_tb(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
 
-mdr_cmi2012(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE,
-  ...)
+mdr_cmi2012(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
 
-eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
-  verbose = FALSE, ...)
+eucast_exceptional_phenotypes(
+  x = NULL,
+  only_sir_columns = any(is.sir(x)),
+  verbose = FALSE,
+  ...
+)
 ```
 
 ## Arguments
@@ -152,25 +168,32 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
 
 ## Value
 
-\- 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
+- 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
 
 ## Details