mirror of
https://github.com/msberends/AMR.git
synced 2025-12-15 23:10:28 +01:00
84 lines
2.0 KiB
Markdown
84 lines
2.0 KiB
Markdown
# 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"
|
||
```
|