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Add add_if_missing parameter to control NA handling in interpretive rules (#264)

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Matthijs Berends
2026-04-21 21:53:43 +02:00
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parent fb8758f36b
commit 8ff5d4472a
46 changed files with 1232 additions and 1016 deletions
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6
man/clinical_breakpoints.Rd
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@@ -8,9 +8,9 @@
A \link[tibble:tibble]{tibble} with 45 730 observations and 14 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{type}\cr Breakpoint type, either {.val ECOFF}, {.val animal}, or {.val human}
\item \code{host}\cr Host of infectious agent. This is mostly useful for veterinary breakpoints and is either {.val ECOFF}, {.val aquatic}, {.val cats}, {.val cattle}, {.val dogs}, {.val horse}, {.val human}, {.val poultry}, or {.val swine}
\item \code{method}\cr Testing method, either {.val DISK} or {.val MIC}
\item \code{type}\cr Breakpoint type, either \code{"ECOFF"}, \code{"animal"}, or \code{"human"}
\item \code{host}\cr Host of infectious agent. This is mostly useful for veterinary breakpoints and is either \code{"ECOFF"}, \code{"aquatic"}, \code{"cats"}, \code{"cattle"}, \code{"dogs"}, \code{"horse"}, \code{"human"}, \code{"poultry"}, or \code{"swine"}
\item \code{method}\cr Testing method, either \code{"DISK"} or \code{"MIC"}
\item \code{site}\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"
\item \code{mo}\cr Microbial ID, see \code{\link[=as.mo]{as.mo()}}
\item \code{rank_index}\cr Taxonomic rank index of \code{mo} from 1 (subspecies/infraspecies) to 5 (unknown microorganism)