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(v2.1.1.9163) cleanup

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dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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24
man/antimicrobial_selectors.Rd
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@@ -2,8 +2,6 @@
% Please edit documentation in R/amr_selectors.R
\name{antimicrobial_selectors}
\alias{antimicrobial_selectors}
\alias{amr_class}
\alias{amr_selector}
\alias{aminoglycosides}
\alias{aminopenicillins}
\alias{antifungals}
@@ -35,17 +33,13 @@
\alias{tetracyclines}
\alias{trimethoprims}
\alias{ureidopenicillins}
\alias{amr_class}
\alias{amr_selector}
\alias{administrable_per_os}
\alias{administrable_iv}
\alias{not_intrinsic_resistant}
\title{Antimicrobial Selectors}
\usage{
amr_class(amr_class, only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
amr_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
@@ -114,6 +108,12 @@ trimethoprims(only_sir_columns = FALSE, return_all = TRUE, ...)
ureidopenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
amr_class(amr_class, only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
amr_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
administrable_per_os(only_sir_columns = FALSE, return_all = TRUE, ...)
administrable_iv(only_sir_columns = FALSE, return_all = TRUE, ...)
@@ -122,8 +122,6 @@ not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
version_expertrules = 3.3, ...)
}
\arguments{
\item{amr_class}{an antimicrobial class or a part of it, such as \code{"carba"} and \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
\item{only_sir_columns}{a \link{logical} to indicate whether only columns of class \code{sir} must be selected (default is \code{FALSE}), see \code{\link[=as.sir]{as.sir()}}}
\item{only_treatable}{a \link{logical} to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})}
@@ -132,6 +130,8 @@ not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
\item{...}{ignored, only in place to allow future extensions}
\item{amr_class}{an antimicrobial class or a part of it, such as \code{"carba"} and \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
\item{filter}{an \link{expression} to be evaluated in the \link{antibiotics} data set, such as \code{name \%like\% "trim"}}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
@@ -160,10 +160,10 @@ All columns in the data in which these functions are called will be searched for
The \code{\link[=amr_class]{amr_class()}} function can be used to filter/select on a manually defined antimicrobial class. It searches for results in the \link{antibiotics} data set within the columns \code{group}, \code{atc_group1} and \code{atc_group2}.
The \code{\link[=amr_selector]{amr_selector()}} function can be used to internally filter the \link{antibiotics} data set on any results, see \emph{Examples}. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
The \code{\link[=administrable_per_os]{administrable_per_os()}} and \code{\link[=administrable_iv]{administrable_iv()}} functions also rely on the \link{antibiotics} data set - antimicrobials will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the \link{antibiotics} data set.
The \code{\link[=amr_selector]{amr_selector()}} function can be used to internally filter the \link{antibiotics} data set on any results, see \emph{Examples}. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
}
\section{Full list of supported (antimicrobial) classes}{