guess_ab_col: Guess Antibiotic Column

In msberends/AMR: Antimicrobial Resistance Data Analysis

Guess Antibiotic Column

Description

This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations.

Usage

guess_ab_col(x = NULL, search_string = NULL, verbose = FALSE,
  only_sir_columns = 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
only_sir_columns	a logical to indicate whether only antibiotic columns must be detected that were transformed to class sir (see as.sir()) on beforehand (default is FALSE)

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.

Value

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

Examples

df <- data.frame(
  amox = "S",
  tetr = "R"
)

guess_ab_col(df, "amoxicillin")
guess_ab_col(df, "J01AA07") # ATC code of tetracycline

guess_ab_col(df, "J01AA07", verbose = TRUE)
# NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).

# WHONET codes
df <- data.frame(
  AMP_ND10 = "R",
  AMC_ED20 = "S"
)
guess_ab_col(df, "ampicillin")
guess_ab_col(df, "J01CR02")
guess_ab_col(df, as.ab("augmentin"))

msberends/AMR documentation built on March 5, 2025, 2:28 p.m.