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.

Maturing lifecycle

The lifecycle of this function is maturing. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.

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

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"