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(v3.0.0.9003) eucast_rules fix, new tidymodels integration

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dr. M.S. (Matthijs) Berends
2025-06-13 14:03:21 +02:00
parent 3742e9e994
commit 72db2b2562
22 changed files with 760 additions and 107 deletions
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man/as.sir.Rd
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@ -247,7 +247,7 @@ To determine which isolates are multi-drug resistant, be sure to run \code{\link
The function \code{\link[=is.sir]{is.sir()}} detects if the input contains class \code{sir}. If the input is a \link{data.frame} or \link{list}, it iterates over all columns/items and returns a \link{logical} vector.
The base R function \code{\link[=as.double]{as.double()}} can be used to retrieve quantitative values from a \code{sir} object: \code{"S"} = 1, \code{"I"}/\code{"SDD"} = 2, \code{"R"} = 3. All other values are rendered \code{NA} . \strong{Note:} Do not use \code{as.integer()}, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.
The base R function \code{\link[=as.double]{as.double()}} can be used to retrieve quantitative values from a \code{sir} object: \code{"S"} = 1, \code{"I"}/\code{"SDD"} = 2, \code{"R"} = 3. All other values are rendered \code{NA}. \strong{Note:} Do not use \code{as.integer()}, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.
The function \code{\link[=is_sir_eligible]{is_sir_eligible()}} returns \code{TRUE} when a column contains at most 5\% potentially invalid antimicrobial interpretations, and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} argument. If the input is a \link{data.frame}, it iterates over all columns and returns a \link{logical} vector.
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