mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 18:46:13 +01:00
47 lines
1.7 KiB
R
47 lines
1.7 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(tbl = NULL, col = NULL, verbose = FALSE)
|
|
}
|
|
\arguments{
|
|
\item{tbl}{a \code{data.frame}}
|
|
|
|
\item{col}{a character to look for}
|
|
|
|
\item{verbose}{a logical to indicate whether additional info should be printed}
|
|
}
|
|
\description{
|
|
This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set. Also supports WHONET abbreviations. You can look for an antibiotic (trade) name or abbreviation and it will search the \code{data.frame} for any column containing a name or ATC code of that antibiotic.
|
|
}
|
|
\section{Read more on our website!}{
|
|
|
|
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
|
}
|
|
|
|
\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)
|
|
# using column `tetr` for col "J01AA07"
|
|
# [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.atc("augmentin"))
|
|
# [1] "AMC_ED20"
|
|
}
|