as.disk: Transform Input to Disk Diffusion Diameters

In AMR: Antimicrobial Resistance Data Analysis

Transform Input to Disk Diffusion Diameters

Description

This transforms a vector to a new class disk, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.

Usage

as.disk(x, na.rm = FALSE)

NA_disk_

is.disk(x)

Arguments

x	vector
na.rm	a logical indicating whether missing values should be removed

Format

An object of class disk (inherits from integer) of length 1.

Details

Interpret disk values as SIR values with as.sir(). It supports guidelines from EUCAST and CLSI.

Disk diffusion growth zone sizes must be between 6 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 6-50 range will return NA.

NA_disk_ is a missing value of the new disk class.

Value

An integer with additional class disk

See Also

as.sir()

Examples

# transform existing disk zones to the `disk` class (using base R)
df <- data.frame(
  microorganism = "Escherichia coli",
  AMP = 20,
  CIP = 14,
  GEN = 18,
  TOB = 16
)
df[, 2:5] <- lapply(df[, 2:5], as.disk)
str(df)


# transforming is easier with dplyr:
if (require("dplyr")) {
  df %>% mutate(across(AMP:TOB, as.disk))
}


# interpret disk values, see ?as.sir
as.sir(
  x = as.disk(18),
  mo = "Strep pneu", # `mo` will be coerced with as.mo()
  ab = "ampicillin", # and `ab` with as.ab()
  guideline = "EUCAST"
)

# interpret whole data set, pretend to be all from urinary tract infections:
as.sir(df, uti = TRUE)

AMR documentation built on Oct. 22, 2023, 1:08 a.m.