(v1.4.0.9050) ab selectors base R

man/antibiotic_class_selectors.Rd

@@ -50,12 +50,10 @@ tetracyclines()
 \item{ab_class}{an antimicrobial class, like \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.}
 }
 \description{
-Use these selection helpers inside any function that allows \href{https://tidyselect.r-lib.org/reference/language.html}{Tidyverse selection helpers}, such as \code{\link[dplyr:select]{select()}} and \code{\link[tidyr:pivot_longer]{pivot_longer()}}. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
+These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
 }
 \details{
 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.
-
-\strong{N.B. These functions require the \code{tidyselect} package to be installed}, that comes with the \code{dplyr} package. An error will be thrown if the \code{tidyselect} package is not installed, or if the functions are used outside a function that allows \href{https://tidyselect.r-lib.org/reference/language.html}{Tidyverse selection helpers} such as \code{\link[dplyr:select]{select()}} and \code{\link[tidyr:pivot_longer]{pivot_longer()}}`.
 }
 \section{Reference data publicly available}{
 
@@ -68,6 +66,14 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
 }
 
 \examples{
+# `example_isolates` is a dataset available in the AMR package.
+# See ?example_isolates.
+
+# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
+example_isolates[, c(carbapenems())]
+# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
+example_isolates[, c("mo", aminoglycosides())]
+
 if (require("dplyr")) {
 
   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):

man/first_isolate.Rd

@@ -50,7 +50,7 @@ filter_first_weighted_isolate(
 )
 }
 \arguments{
-\item{x}{a \link{data.frame} containing isolates. Can be omitted when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.}
+\item{x}{a \link{data.frame} containing isolates. Can be left blank when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.}
 
 \item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column with a date class}
 
@@ -93,7 +93,7 @@ A \code{\link{logical}} vector
 Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package.
 }
 \details{
-These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be omitted, please see \emph{Examples}.
+These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be left blank, please see \emph{Examples}.
 
 The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but more efficient for data sets containing microorganism codes or names.
 

man/key_antibiotics.Rd

@@ -40,7 +40,7 @@ key_antibiotics_equal(
 )
 }
 \arguments{
-\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be omitted when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}.}
+\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}.}
 
 \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
 
@@ -68,7 +68,7 @@ key_antibiotics_equal(
 These function can be used to determine first isolates (see \code{\link[=first_isolate]{first_isolate()}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first \emph{weighted} isolates.
 }
 \details{
-The \code{\link[=key_antibiotics]{key_antibiotics()}} function is context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be omitted, please see \emph{Examples}.
+The \code{\link[=key_antibiotics]{key_antibiotics()}} function is context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be left blank, please see \emph{Examples}.
 
 The function \code{\link[=key_antibiotics]{key_antibiotics()}} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antibiotics]{key_antibiotics()}} and ignored by \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}}.
 

man/mdro.Rd

@@ -40,7 +40,7 @@ mdr_cmi2012(x, guideline = "CMI2012", ...)
 eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
 }
 \arguments{
-\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be omitted when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.}
+\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.}
 
 \item{guideline}{a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, please see \emph{Details}.}
 
@@ -72,7 +72,7 @@ Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed}
 Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
 }
 \details{
-These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be omitted, please see \emph{Examples}.
+These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be left blank, please see \emph{Examples}.
 
 For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).
 

man/mo_property.Rd

@@ -85,7 +85,7 @@ mo_url(x, open = FALSE, language = get_locale(), ...)
 mo_property(x, property = "fullname", language = get_locale(), ...)
 }
 \arguments{
-\item{x}{any character (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be omitted for auto-guessing the column containing microorganism codes when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}, please see \emph{Examples}.}
+\item{x}{any character (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be left blank for auto-guessing the column containing microorganism codes when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}, please see \emph{Examples}.}
 
 \item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can be overwritten by setting the option \code{AMR_locale}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Also used to translate text like "no growth". Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 

man/resistance_predict.Rd

@@ -47,7 +47,7 @@ ggplot_rsi_predict(
 )
 }
 \arguments{
-\item{x}{a \link{data.frame} containing isolates. Can be omitted when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.}
+\item{x}{a \link{data.frame} containing isolates. Can be left blank when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.}
 
 \item{col_ab}{column name of \code{x} containing antimicrobial interpretations (\code{"R"}, \code{"I"} and \code{"S"})}