P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 21:22:01 +02:00
Code Releases Activity

(v1.7.1.9013) temp fix for ggplot2 bug #4511

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-07-04 22:10:46 +02:00
parent 350dbe6a11
commit 16b4c74d44
37 changed files with 488 additions and 365 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
man/ab_property.Rd
View File

@ -17,7 +17,7 @@
\alias{ab_url}
\title{Get Properties of an Antibiotic}
\usage{
ab_name(x, language = get_locale(), tolower = FALSE, ...)
ab_name(x, language = get_locale(), tolower = FALSE, snake_case = FALSE, ...)
ab_atc(x, ...)
@ -50,6 +50,8 @@ ab_property(x, property = "name", language = get_locale(), ...)
\item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}. This will lead to e.g. "polymyxin B" and not "polymyxin b".}
\item{snake_case}{a \link{logical} to indicate whether the names should be returned in so-called \href{https://en.wikipedia.org/wiki/Snake_case}{snake case}: in lower case and all spaces/slashes replaced with an underscore (\verb{_}). This is useful for column renaming.}
\item{...}{other arguments passed on to \code{\link[=as.ab]{as.ab()}}}
\item{administration}{way of administration, either \code{"oral"} or \code{"iv"}}

2
man/antibiotic_class_selectors.Rd
View File

@ -82,7 +82,7 @@ ureidopenicillins(only_rsi_columns = FALSE)
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{
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}.
These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, 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.
}