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(v2.1.1.9217) allow + in amr selectors

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dr. M.S. (Matthijs) Berends
2025-03-18 16:35:22 +01:00
parent 8d8444c607
commit 4dc4398ad1
23 changed files with 543 additions and 440 deletions
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36
man/antibiogram.Rd
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@ -28,13 +28,11 @@ antibiogram(x, antimicrobials = where(is.sir), mo_transform = "shortname",
info = interactive(), ...)
wisca(x, antimicrobials = where(is.sir), ab_transform = "name",
syndromic_group = NULL, add_total_n = FALSE, only_all_tested = FALSE,
digits = 1,
syndromic_group = NULL, digits = 1,
formatting_type = getOption("AMR_antibiogram_formatting_type", 14),
col_mo = NULL, language = get_AMR_locale(), minimum = 30,
combine_SI = TRUE, sep = " + ", simulations = 1000,
conf_interval = 0.95, interval_side = "two-tailed",
info = interactive(), ...)
col_mo = NULL, language = get_AMR_locale(), combine_SI = TRUE,
sep = " + ", simulations = 1000, conf_interval = 0.95,
interval_side = "two-tailed", info = interactive(), ...)
retrieve_wisca_parameters(wisca_model, ...)
@ -48,7 +46,25 @@ retrieve_wisca_parameters(wisca_model, ...)
\arguments{
\item{x}{a \link{data.frame} containing at least a column with microorganisms and columns with antimicrobial results (class 'sir', see \code{\link[=as.sir]{as.sir()}})}
\item{antimicrobials}{vector of any antimicrobial name or code (will be evaluated with \code{\link[=as.ab]{as.ab()}}, column name of \code{x}, or (any combinations of) \link[=antimicrobial_selectors]{antimicrobial selectors} such as \code{\link[=aminoglycosides]{aminoglycosides()}} or \code{\link[=carbapenems]{carbapenems()}}. For combination antibiograms, this can also be set to values separated with \code{"+"}, such as \code{"TZP+TOB"} or \code{"cipro + genta"}, given that columns resembling such antimicrobials exist in \code{x}. See \emph{Examples}.}
\item{antimicrobials}{a vector specifying the antimicrobials to include in the antibiogram (see \emph{Examples}). Will be evaluated using \code{\link[=guess_ab_col]{guess_ab_col()}}. This can be:
\itemize{
\item Any antimicrobial name or code
\item A column name in \code{x} that contains SIR values
\item Any \link[=antimicrobial_selectors]{antimicrobial selector}, such as \code{\link[=aminoglycosides]{aminoglycosides()}} or \code{\link[=carbapenems]{carbapenems()}}
\item A combination of the above, using \code{c()}, e.g.:
\itemize{
\item \code{c(aminoglycosides(), "AMP", "AMC")}
\item \code{c(aminoglycosides(), carbapenems())}
}
\item Combination therapy, indicated by using \code{"+"}, with or without \link[=antimicrobial_selectors]{antimicrobial selectors}, e.g.:
\itemize{
\item \code{"TZP+TOB"}
\item \code{"cipro + genta"}
\item \code{carbapenems() + "GEN"}
\item \code{carbapenems() + c("", "GEN")}
\item \code{carbapenems() + c("", aminoglycosides())}
}
}}
\item{mo_transform}{a character to transform microorganism input - must be \code{"name"}, \code{"shortname"} (default), \code{"gramstain"}, or one of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be \code{NULL} to not transform the input or \code{NA} to consider all microorganisms 'unknown'.}
@ -361,6 +377,12 @@ antibiogram(example_isolates,
mo_transform = "gramstain"
)
# you can use any antimicrobial selector with `+` too:
antibiogram(example_isolates,
antimicrobials = ureidopenicillins() + c("", "GEN", "tobra"),
mo_transform = "gramstain"
)
# names of antimicrobials do not need to resemble columns exactly:
antibiogram(example_isolates,
antimicrobials = c("Cipro", "cipro + genta"),

2
man/antimicrobial_selectors.Rd
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@ -148,7 +148,7 @@ not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
When used inside selecting or filtering, this returns a \link{character} vector of column names, with additional class \code{"amr_selector"}. When used individually, this returns an \link[=as.ab]{'ab' vector} with all possible antimicrobials that the function would be able to select or filter.
}
\description{
These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations.
These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base \R, tidyverse, tidymodels, and \code{data.table}.
In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up using: