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.

guess_ab_col(x = NULL, search_string = NULL, verbose = FALSE)

Arguments

x	a data.frame
search_string	a text to search x for, will be checked with as.ab if this value is not a column in x
verbose	a logical to indicate whether additional info should be printed

Value

A column name of x, or NULL when no result is found.

Details

You can look for an antibiotic (trade) name or abbreviation and it will search x and the antibiotics data set for any column containing a name or code of that antibiotic. Longer columns names take precendence over shorter column names.

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a 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)
# Note: Using column `tetr` as input for "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.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"
# }