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()). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.

Usage

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 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()) - the default is the first column of class mo. Values will be coerced using as.mo().

• 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 to indicate whether only antimicrobial columns must be included that were transformed to class sir on beforehand. Defaults to FALSE if no columns of x have a class sir.

• ...:

  Ignored, only in place to allow future extensions.

• y, z:

  character vectors to compare.

• type:

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

• ignore_I:

  logical 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 call, see Examples.

The function key_antimicrobials() returns a character vector with 12 antimicrobial results for every isolate. The function all_antimicrobials() returns a character 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() 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()

Examples

# `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
# }