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reference/guess_ab_col.md

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+# 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"
+```