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 4 0.25 1 8 0.0625 0.025 32 2
#> [10] 0.5 0.5 0.002 <=0.001 0.025 32 64 64 0.01
#> [19] 2 0.01 1 1 0.25 0.25 1
random_disk(25)
#> Class <disk>
#> [1] 42 21 30 37 26 39 18 43 46 10 39 40 35 45 48 15 21 40 45 42 10 9 6 14 26
random_rsi(25)
#> Class <rsi>
#> [1] I I S S S R R R S R S I R R R R I I R R S I R S S
# \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] 32 0.002 128 0.002 16 0.002 16 128 0.01
#> [10] <=0.001 0.002 0.25 0.0625 2 0.5 2 16 2
#> [19] 0.025 1 0.025 128 0.002 0.25 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 0.25 0.25 2 0.25 0.25 1 0.25 1 0.25 16 0.5 2 1 0.5 0.5
#> [16] 0.25 1 8 4 0.25 0.5 16 1 1 0.25
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] >=4 0.5 2 0.25 1 0.25 <=0.125 1 1
#> [10] >=4 0.25 0.5 0.5 0.25 0.5 <=0.125 0.5 2
#> [19] 1 0.25 2 <=0.125 0.5 0.25 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 39 13 39 41 42 49 49 43 42 43 50 43 21 34 21 34 13 23 12 18 26 49 46 45 23
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 14 16 15 11 16 12 17 17 13 13 16 17 12 14 16 14 11 11 17 14 17 11 16 17 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 27 19 22 23 17 20 17 20 25 20 16 18 27 24 16 16 27 20 17 27 20 26 20 18 22
# }