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(v1.7.1.9026) updated DDDs
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@ -92,7 +92,7 @@ trimethoprims(only_rsi_columns = FALSE, ...)
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ureidopenicillins(only_rsi_columns = FALSE, ...)
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}
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\arguments{
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\item{ab_class}{an antimicrobial class, such as \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.}
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\item{ab_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.}
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\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \verb{<rsi>} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
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@ -113,7 +113,7 @@ These functions can be used in data set calls for selecting columns and filterin
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All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the \link{antibiotics} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
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The \code{\link[=ab_class]{ab_class()}} function can be used to filter/select on a manually defined antibiotic class. It searches for results in the \link{antibiotics} data set within the columns \code{name}, \code{atc_group1} and \code{atc_group2}.
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The \code{\link[=ab_class]{ab_class()}} function can be used to filter/select on a manually defined antibiotic class. It searches for results in the \link{antibiotics} data set within the columns \code{group}, \code{atc_group1} and \code{atc_group2}.
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The \code{\link[=ab_selector]{ab_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.
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@ -204,6 +204,10 @@ example_isolates[any(carbapenems() == "R"), penicillins()]
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# and erythromycin is not a penicillin:
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example_isolates[, penicillins() & administrable_per_os()]
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# ab_selector() applies a filter in the `antibiotics` data set and is thus very
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# flexible. For instance, to select antibiotic columns with an oral DDD of at
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# least 1 gram:
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example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
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# dplyr -------------------------------------------------------------------
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\donttest{
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