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(v2.1.1.9157) improved as.ab(), fixed knit_print of antibiogram

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dr. M.S. (Matthijs) Berends
2025-02-26 13:27:20 +01:00
parent b10989f431
commit 195dfb4b91
20 changed files with 107 additions and 42 deletions
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2
man/antimicrobial_selectors.Rd
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@ -154,7 +154,7 @@ my_data_with_all_these_columns \%>\%
\details{
These functions can be used in data set calls for selecting columns and filtering rows. They work with base \R, the Tidyverse, and \code{data.table}. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but are not limited to \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 selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html}{our tutorial} on using these AMR functions for predictive modelling.
All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling.
All columns in the data in which these functions are called will be searched for known antimicrobial 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.

3
man/as.ab.Rd
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@ -4,11 +4,14 @@
\alias{as.ab}
\alias{ab}
\alias{is.ab}
\alias{ab_reset_session}
\title{Transform Input to an Antibiotic ID}
\usage{
as.ab(x, flag_multiple_results = TRUE, info = interactive(), ...)
is.ab(x)
ab_reset_session()
}
\arguments{
\item{x}{a \link{character} vector to determine to antibiotic ID}