AMR/man/guess_ab_col.Rd

% 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"
}