mirror of https://github.com/msberends/AMR.git
48 lines
1.7 KiB
R
48 lines
1.7 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/guess_ab_col.R
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\name{guess_ab_col}
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\alias{guess_ab_col}
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\title{Guess antibiotic column}
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\usage{
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guess_ab_col(tbl = NULL, col = NULL, verbose = FALSE)
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}
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\arguments{
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\item{tbl}{a \code{data.frame}}
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\item{col}{a character to look for}
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\item{verbose}{a logical to indicate whether additional info should be printed}
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}
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\description{
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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.
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}
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\section{Read more on our website!}{
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\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
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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}.
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}
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\examples{
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df <- data.frame(amox = "S",
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tetr = "R")
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guess_ab_col(df, "amoxicillin")
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# [1] "amox"
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guess_ab_col(df, "J01AA07") # ATC code of Tetracycline
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# [1] "tetr"
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guess_ab_col(df, "J01AA07", verbose = TRUE)
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# using column `tetr` for col "J01AA07"
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# [1] "tetr"
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# WHONET codes
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df <- data.frame(AMP_ND10 = "R",
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AMC_ED20 = "S")
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guess_ab_col(df, "ampicillin")
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# [1] "AMP_ND10"
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guess_ab_col(df, "J01CR02")
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# [1] "AMC_ED20"
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guess_ab_col(df, as.atc("augmentin"))
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# [1] "AMC_ED20"
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}
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