These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.
Usage
random_mic(size = NULL, mo = NULL, ab = NULL, ...)
random_disk(size = NULL, mo = NULL, ab = NULL, ...)
random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...)Arguments
- size
desired size of the returned vector. If used in a data.frame call or
dplyrverb, will get the current (group) size if left blank.- mo
any character that can be coerced to a valid microorganism code with
as.mo()- ab
any character that can be coerced to a valid antimicrobial agent code with
as.ab()- ...
ignored, only in place to allow future extensions
- prob_RSI
a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)
Value
class <mic> for random_mic() (see as.mic()) and class <disk> for random_disk() (see as.disk())
Details
The base R function sample() is used for generating values.
Generated values are based on the EUCAST 2022 guideline as implemented in the rsi_translation data set. To create specific generated values per bug or drug, set the mo and/or ab argument.
Examples
random_mic(25)
#> Class <mic>
#> [1] 32 1 0.001 0.25 1 16 0.0625 64 0.25 2
#> [11] 4 0.01 0.125 8 128 0.0625 >=256 0.025 >=256 0.125
#> [21] 64 32 0.0625 1 4
random_disk(25)
#> Class <disk>
#> [1] 15 46 30 46 39 44 18 22 8 28 24 30 14 20 47 46 10 41 46 21 23 47 13 25 49
random_rsi(25)
#> Class <rsi>
#> [1] R R R I S S S S S R R R I R S S S I R S I R S I I
# \donttest{
# make the random generation more realistic by setting a bug and/or drug:
random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
#> Class <mic>
#> [1] 0.5 64 0.005 32 4 0.005 128 0.25 64 0.025 0.5 2
#> [13] 0.025 0.025 2 0.125 64 8 2 1 0.125 64 32 32
#> [25] 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 8 4 8 8 2 8 1 0.5 16 2
#> [11] 8 16 <=0.25 0.5 8 8 1 2 2 <=0.25
#> [21] 8 8 2 2 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.25 8 0.125 8 16 4 8 0.025 8 4 8 4
#> [13] 0.125 0.125 0.25 1 0.025 8 0.025 1 2 4 4 0.25
#> [25] 4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 35 48 23 48 32 44 49 43 11 18 41 37 30 22 19 26 40 50 15 30 41 41 42 21 15
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 15 16 13 12 16 11 12 16 17 15 14 13 12 13 15 16 15 13 16 14 16 16 17 16 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 25 18 18 18 24 15 20 19 20 21 26 22 18 15 23 21 19 22 26 25 21 23 20 16 23
# }