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(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()

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dr. M.S. (Matthijs) Berends
2026-04-02 11:42:19 +02:00
parent 3a736bc484
commit 26613d774b
33 changed files with 1765 additions and 1584 deletions
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man/as.sir.Rd
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@@ -138,7 +138,7 @@ The default \code{"conservative"} setting ensures cautious handling of uncertain
\item{include_PKPD}{A \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{breakpoint_type}{The type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}
\item{breakpoint_type}{The type of breakpoints to use, either {.val ECOFF}, {.val animal}, or {.val human}. ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}
\item{host}{A vector (or column name) with \link{character}s to indicate the host. Only useful for veterinary breakpoints, as it requires \code{breakpoint_type = "animal"}. The values can be any text resembling the animal species, even in any of the 28 supported languages of this package. For foreign languages, be sure to set the language with \code{\link[=set_AMR_locale]{set_AMR_locale()}} (though it will be automatically guessed based on the system language).}