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mirror of https://github.com/msberends/AMR.git synced 2025-07-08 18:41:58 +02:00

(v1.7.1.9005) ab class selectors for R-3.0 and R-3.1

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2021-06-22 12:16:42 +02:00
parent c44d9392ca
commit d04e83f494
41 changed files with 227 additions and 279 deletions

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@ -79,12 +79,10 @@ ureidopenicillins(only_rsi_columns = FALSE)
\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()}}}
}
\description{
These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(getRversion() < "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, "."), "")}}
These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
}
\details{
\strong{\Sexpr{ifelse(getRversion() < "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, "."), "")}}
These functions can be used in data set calls for selecting columns and filtering rows, see \emph{Examples}. They support base R, but work more convenient in dplyr functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}.
These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the \href{https://tidyselect.r-lib.org/reference/language.html}{Tidyverse selection helpers}, but also work in base \R and not only in \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}.
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.) in 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. Use the \code{\link[=ab_class]{ab_class()}} function to filter/select on a manually defined antibiotic class.
}

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@ -181,11 +181,8 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
example_isolates[first_isolate(example_isolates), ]
\donttest{
# faster way, only works in R 3.2 and later:
example_isolates[first_isolate(), ]
\donttest{
# get all first Gram-negatives
example_isolates[which(first_isolate() & mo_is_gram_negative()), ]

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@ -41,7 +41,7 @@ Join the data set \link{microorganisms} easily to an existing data set or to a \
\details{
\strong{Note:} As opposed to the \code{join()} functions of \code{dplyr}, \link{character} vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix.
If the \code{dplyr} package is installed, their join functions will be used. Otherwise, the much slower \code{\link[=merge]{merge()}} and \code{\link[=interaction]{interaction()}} functions from base R will be used.
If the \code{dplyr} package is installed, their join functions will be used. Otherwise, the much slower \code{\link[=merge]{merge()}} and \code{\link[=interaction]{interaction()}} functions from base \R will be used.
}
\section{Stable Lifecycle}{

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@ -158,7 +158,7 @@
The \code{ggplot} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model that is extendible with any \code{ggplot2} function.
}
\description{
Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support for base R and \code{ggplot2}.
Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support for base \R and \code{ggplot2}.
}
\details{
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.

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@ -31,7 +31,7 @@ class \verb{<mic>} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[
These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.
}
\details{
The base R function \code{\link[=sample]{sample()}} is used for generating values.
The base \R function \code{\link[=sample]{sample()}} is used for generating values.
Generated values are based on the latest EUCAST guideline implemented in the \link{rsi_translation} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument.
}