guess_ab_col {AMR} | R Documentation |
Guess Antibiotic Column
Description
This tries to find a column name in a data set based on information from the antimicrobials 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 |
verbose |
A logical to indicate whether additional info should be printed. |
only_sir_columns |
A logical to indicate whether only antimicrobial columns must be included that were transformed to class sir on beforehand. Defaults to |
Details
You can look for an antibiotic (trade) name or abbreviation and it will search x
and the antimicrobials 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)
# 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, "augmentin")
[Package AMR version 3.0.0 Index]