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 antibiotics data set. Also supports WHONET abbreviations.
Usage
guess_ab_col(
x = NULL,
search_string = NULL,
verbose = FALSE,
only_sir_columns = FALSE
)
Arguments
x |
|
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 antibiotic columns must be detected that were transformed to class |
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"))
[Package AMR version 2.1.1 Index]