mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 20:06:12 +01:00
67 lines
1.9 KiB
R
67 lines
1.9 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/guess_ab_col.R
|
|
\name{guess_ab_col}
|
|
\alias{guess_ab_col}
|
|
\title{Guess Antibiotic Column}
|
|
\usage{
|
|
guess_ab_col(
|
|
x = NULL,
|
|
search_string = NULL,
|
|
verbose = FALSE,
|
|
only_rsi_columns = FALSE
|
|
)
|
|
}
|
|
\arguments{
|
|
\item{x}{a \link{data.frame}}
|
|
|
|
\item{search_string}{a text to search \code{x} for, will be checked with \code{\link[=as.ab]{as.ab()}} if this value is not a column in \code{x}}
|
|
|
|
\item{verbose}{a \link{logical} to indicate whether additional info should be printed}
|
|
|
|
\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \verb{<rsi>} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
|
|
}
|
|
\value{
|
|
A column name of \code{x}, or \code{NULL} when no result is found.
|
|
}
|
|
\description{
|
|
This tries to find a column name in a data set based on information from the \link{antibiotics} data set. Also supports WHONET abbreviations.
|
|
}
|
|
\details{
|
|
You can look for an antibiotic (trade) name or abbreviation and it will search \code{x} and the \link{antibiotics} data set for any column containing a name or code of that antibiotic. \strong{Longer columns names take precedence over shorter column names.}
|
|
}
|
|
\examples{
|
|
df <- data.frame(
|
|
amox = "S",
|
|
tetr = "R"
|
|
)
|
|
|
|
guess_ab_col(df, "amoxicillin")
|
|
# [1] "amox"
|
|
guess_ab_col(df, "J01AA07") # ATC code of tetracycline
|
|
# [1] "tetr"
|
|
|
|
guess_ab_col(df, "J01AA07", verbose = TRUE)
|
|
# NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).
|
|
# [1] "tetr"
|
|
|
|
# WHONET codes
|
|
df <- data.frame(
|
|
AMP_ND10 = "R",
|
|
AMC_ED20 = "S"
|
|
)
|
|
guess_ab_col(df, "ampicillin")
|
|
# [1] "AMP_ND10"
|
|
guess_ab_col(df, "J01CR02")
|
|
# [1] "AMC_ED20"
|
|
guess_ab_col(df, as.ab("augmentin"))
|
|
# [1] "AMC_ED20"
|
|
|
|
# Longer names take precendence:
|
|
df <- data.frame(
|
|
AMP_ED2 = "S",
|
|
AMP_ED20 = "S"
|
|
)
|
|
guess_ab_col(df, "ampicillin")
|
|
# [1] "AMP_ED20"
|
|
}
|