AMR/reference/key_antimicrobials.md

# (Key) Antimicrobials for First Weighted Isolates

These functions can be used to determine first weighted isolates by
considering the phenotype for isolate selection (see
[`first_isolate()`](https://amr-for-r.org/reference/first_isolate.md)).
Using a phenotype-based method to determine first isolates is more
reliable than methods that disregard phenotypes.

## Usage

``` r
key_antimicrobials(x = NULL, col_mo = NULL, universal = c("ampicillin",
  "amoxicillin/clavulanic acid", "cefuroxime", "piperacillin/tazobactam",
  "ciprofloxacin", "trimethoprim/sulfamethoxazole"),
  gram_negative = c("gentamicin", "tobramycin", "colistin", "cefotaxime",
  "ceftazidime", "meropenem"), gram_positive = c("vancomycin", "teicoplanin",
  "tetracycline", "erythromycin", "oxacillin", "rifampin"),
  antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole",
  "nystatin", "voriconazole"), only_sir_columns = any(is.sir(x)), ...)

all_antimicrobials(x = NULL, only_sir_columns = any(is.sir(x)), ...)

antimicrobials_equal(y, z, type = c("points", "keyantimicrobials"),
  ignore_I = TRUE, points_threshold = 2, ...)
```

## Arguments

- x:

  A [data.frame](https://rdrr.io/r/base/data.frame.html) with
  antimicrobials columns, like `AMX` or `amox`. Can be left blank to
  determine automatically.

- col_mo:

  Column name of the names or codes of the microorganisms (see
  [`as.mo()`](https://amr-for-r.org/reference/as.mo.md)) - the default
  is the first column of class
  [`mo`](https://amr-for-r.org/reference/as.mo.md). Values will be
  coerced using [`as.mo()`](https://amr-for-r.org/reference/as.mo.md).

- universal:

  Names of **broad-spectrum** antimicrobial drugs, case-insensitive. Set
  to `NULL` to ignore. See *Details* for the default antimicrobial
  drugs.

- gram_negative:

  Names of antibiotic drugs for **Gram-positives**, case-insensitive.
  Set to `NULL` to ignore. See *Details* for the default antibiotic
  drugs.

- gram_positive:

  Names of antibiotic drugs for **Gram-negatives**, case-insensitive.
  Set to `NULL` to ignore. See *Details* for the default antibiotic
  drugs.

- antifungal:

  Names of antifungal drugs for **fungi**, case-insensitive. Set to
  `NULL` to ignore. See *Details* for the default antifungal drugs.

- 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).

- ...:

  Ignored, only in place to allow future extensions.

- y, z:

  [character](https://rdrr.io/r/base/character.html) vectors to compare.

- type:

  Type to determine weighed isolates; can be `"keyantimicrobials"` or
  `"points"`, see *Details*.

- ignore_I:

  [logical](https://rdrr.io/r/base/logical.html) to indicate whether
  antibiotic interpretations with `"I"` will be ignored when
  `type = "keyantimicrobials"`, see *Details*.

- points_threshold:

  Minimum number of points to require before differences in the
  antibiogram will lead to inclusion of an isolate when
  `type = "points"`, see *Details*.

## Details

The `key_antimicrobials()` and `all_antimicrobials()` functions are
context-aware. This means that the `x` argument can be left blank if
used inside a [data.frame](https://rdrr.io/r/base/data.frame.html) call,
see *Examples*.

The function `key_antimicrobials()` returns a
[character](https://rdrr.io/r/base/character.html) vector with 12
antimicrobial results for every isolate. The function
`all_antimicrobials()` returns a
[character](https://rdrr.io/r/base/character.html) vector with all
antimicrobial drug results for every isolate. These vectors can then be
compared using `antimicrobials_equal()`, to check if two isolates have
generally the same antibiogram. Missing and invalid values are replaced
with a dot (`"."`) by `key_antimicrobials()` and ignored by
`antimicrobials_equal()`.

Please see the
[`first_isolate()`](https://amr-for-r.org/reference/first_isolate.md)
function how these important functions enable the 'phenotype-based'
method for determination of first isolates.

The default antimicrobial drugs used for **all rows** (set in
`universal`) are:

- Ampicillin

- Amoxicillin/clavulanic acid

- Cefuroxime

- Ciprofloxacin

- Piperacillin/tazobactam

- Trimethoprim/sulfamethoxazole

The default antimicrobial drugs used for **Gram-negative bacteria** (set
in `gram_negative`) are:

- Cefotaxime

- Ceftazidime

- Colistin

- Gentamicin

- Meropenem

- Tobramycin

The default antimicrobial drugs used for **Gram-positive bacteria** (set
in `gram_positive`) are:

- Erythromycin

- Oxacillin

- Rifampin

- Teicoplanin

- Tetracycline

- Vancomycin

The default antimicrobial drugs used for **fungi** (set in `antifungal`)
are:

- Anidulafungin

- Caspofungin

- Fluconazole

- Miconazole

- Nystatin

- Voriconazole

## See also

[`first_isolate()`](https://amr-for-r.org/reference/first_isolate.md)

## Examples

``` r
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.

# output of the `key_antimicrobials()` function could be like this:
strainA <- "SSSRR.S.R..S"
strainB <- "SSSIRSSSRSSS"

# those strings can be compared with:
antimicrobials_equal(strainA, strainB, type = "keyantimicrobials")
#> [1] TRUE
# TRUE, because I is ignored (as well as missing values)

antimicrobials_equal(strainA, strainB, type = "keyantimicrobials", ignore_I = FALSE)
#> [1] FALSE
# FALSE, because I is not ignored and so the 4th [character] differs

# \donttest{
if (require("dplyr")) {
  # set key antimicrobials to a new variable
  my_patients <- example_isolates %>%
    mutate(keyab = key_antimicrobials(antifungal = NULL)) %>% # no need to define `x`
    mutate(
      # now calculate first isolates
      first_regular = first_isolate(col_keyantimicrobials = FALSE),
      # and first WEIGHTED isolates
      first_weighted = first_isolate(col_keyantimicrobials = "keyab")
    )

  # Check the difference in this data set, 'weighted' results in more isolates:
  sum(my_patients$first_regular, na.rm = TRUE)
  sum(my_patients$first_weighted, na.rm = TRUE)
}
#> [1] 1383
# }
```