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(v3.0.1.9019) Wildtype/Non-wildtype support, and start with interpretive_rules()

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Fixes #246
Fixes #254
Fixes #255
Fixes #256
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dr. M.S. (Matthijs) Berends
2026-02-08 23:15:40 +01:00
parent 2df2911cf4
commit ba4c159154
31 changed files with 394 additions and 165 deletions
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man/antibiogram.Rd
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@@ -72,7 +72,7 @@ retrieve_wisca_parameters(wisca_model, ...)
\item{ab_transform}{A character to transform antimicrobial input - must be one of the column names of the \link{antimicrobials} data set (defaults to \code{"name"}): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be \code{NULL} to not transform the input.}
\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case_when]{case_when()}}. See \emph{Examples}.}
\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case-and-replace-when]{case_when()}}. See \emph{Examples}.}
\item{add_total_n}{\emph{(deprecated in favour of \code{formatting_type})} A \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}