# Guess Antibiotic Column

This tries to find a column name in a data set based on information from
the [antimicrobials](https://amr-for-r.org/reference/antimicrobials.md)
data set. Also supports WHONET abbreviations.

## Usage

``` r
guess_ab_col(x = NULL, search_string = NULL, verbose = FALSE,
  only_sir_columns = FALSE)
```

## Arguments

- x:

  A [data.frame](https://rdrr.io/r/base/data.frame.html).

- search_string:

  A text to search `x` for, will be checked with
  [`as.ab()`](https://amr-for-r.org/reference/as.ab.md) if this value is
  not a column in `x`.

- verbose:

  A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
  additional info should be printed.

- only_sir_columns:

  A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
  only antimicrobial columns must be included that were transformed to
  class [sir](https://amr-for-r.org/reference/as.sir.md) on beforehand.
  Defaults to `FALSE` if no columns of `x` have a class
  [sir](https://amr-for-r.org/reference/as.sir.md).

## 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
[antimicrobials](https://amr-for-r.org/reference/antimicrobials.md) data
set for any column containing a name or code of that antibiotic.

## Examples

``` r
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)
#> Auto-guessing columns suitable for analysis
#> ...
#>  OK.
#> ℹ Using column 'amox' as input for AMX (amoxicillin).
#> ℹ Using column 'tetr' as input for TCY (tetracycline).
#> ℹ 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, "augmentin")
#> [1] "AMC_ED20"
```