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(v1.6.0.9044) betalactams() selector

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dr. M.S. (Matthijs) Berends
2021-05-18 00:53:04 +02:00
parent be49131ed7
commit cfb7df823e
28 changed files with 275 additions and 200 deletions
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5
man/antibiotic_class_selectors.Rd
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@ -4,6 +4,7 @@
\alias{antibiotic_class_selectors}
\alias{ab_class}
\alias{aminoglycosides}
\alias{betalactams}
\alias{carbapenems}
\alias{cephalosporins}
\alias{cephalosporins_1st}
@ -23,6 +24,8 @@ ab_class(ab_class, only_rsi_columns = FALSE)
aminoglycosides(only_rsi_columns = FALSE)
betalactams(only_rsi_columns = FALSE)
carbapenems(only_rsi_columns = FALSE)
cephalosporins(only_rsi_columns = FALSE)
@ -61,6 +64,8 @@ These functions help to select the columns of antibiotics that are of a specific
\strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the \link{antibiotics} data set. This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
}
\section{Stable Lifecycle}{

11
man/filter_ab_class.Rd
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@ -3,6 +3,7 @@
\name{filter_ab_class}
\alias{filter_ab_class}
\alias{filter_aminoglycosides}
\alias{filter_betalactams}
\alias{filter_carbapenems}
\alias{filter_cephalosporins}
\alias{filter_1st_cephalosporins}
@ -35,6 +36,14 @@ filter_aminoglycosides(
...
)
filter_betalactams(
x,
result = NULL,
scope = "any",
only_rsi_columns = FALSE,
...
)
filter_carbapenems(
x,
result = NULL,
@ -157,6 +166,8 @@ Filter isolates on results in specific antimicrobial classes. This makes it easy
}
\details{
All columns of \code{x} will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a filter function like e.g. \code{\link[=filter_aminoglycosides]{filter_aminoglycosides()}} will include column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
}
\section{Stable Lifecycle}{