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)
NA_disk_
is.disk(x)Format
An object of class disk (inherits from integer) of length 1.
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.
NA_disk_ is a missing value of the new <disk> class.
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, an argument will be deprecated and first continue to work, but will emit a 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 data analysis, the complete documentation of all functions and an example analysis using WHONET data.
See also
Examples
# \donttest{
# transform existing disk zones to the `disk` class
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)
# }