Guess antibiotic column

This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations. You can look for an antibiotic (trade) name or abbreviation and it will search the data.frame for any column containing a name or ATC code of that antibiotic.

guess_ab_col(tbl = NULL, col = NULL, verbose = FALSE)

Arguments

tbl	a data.frame
col	a character to look for
verbose	a logical to indicate whether additional info should be printed

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

Examples

# NOT RUN {
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"
# }