Transform input to disk diffusion diameters

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.

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

is.disk(x)

Arguments

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

Value

An integer with additional class disk

Details

Interpret disk values as RSI values with as.rsi(). It supports guidelines from EUCAST and CLSI.

Stable lifecycle

The lifecycle of this function is stable. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.

If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.

Read more on our website!

On our website https://msberends.github.io/AMR/ you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions and an example analysis using WHONET data. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!

See also

as.rsi()

Examples

# \donttest{
# transform existing disk zones to the `disk` class
library(dplyr)
df <- data.frame(microorganism = "E. coli",
                 AMP = 20,
                 CIP = 14,
                 GEN = 18,
                 TOB = 16)
df[, 2:5] <- lapply(df[, 2:5], as.disk)
# same with dplyr:
# df %>% mutate(across(AMP:TOB, as.disk))

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