Guess Antibiotic Column

Source: R/guess_ab_col.R

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,
  only_rsi_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_rsi_columns

a logical to indicate whether only antibiotic columns must be detected that were transformed to class <rsi> (see as.rsi()) on beforehand (defaults to FALSE)

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 precedence over shorter column names.

Stable Lifecycle


The lifecycle of this function is stable. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.

If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.

Read more on Our Website!

On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR data analysis, the complete documentation of all functions 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 (tetracycline).
# [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"