Guess antibiotic column

This tries to find a column name in a data set based on information from the antibiotics data set. You can look for an antibiotic (trade) of abbreviation and it will search the data 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 omprehensive tutorial about how to conduct AMR analysis and find the complete documentation of all functions, which reads a lot easier than in R.

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"
# }