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] 1 32 <=0.002 1 32 0.5 16 1 >=256
#> [10] 128 32 32 4 >=256 0.005 0.0625 8 >=256
#> [19] 0.125 2 64 <=0.002 64 0.5 0.005
random_disk(25)
#> Class <disk>
#> [1] 31 42 37 30 8 32 50 16 33 20 11 50 20 43 17 20 21 47 15 48 25 41 18 9 43
random_rsi(25)
#> Class <rsi>
#> [1] I I R S R S S I R I R S R I S S I I S I R 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] 0.002 0.0625 4 0.025 4 0.01 128 0.01 0.25 >=256
#> [11] 8 0.5 0.002 4 0.005 0.5 16 0.0625 0.25 0.5
#> [21] >=256 0.025 >=256 0.125 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 8 <=1 2 >=16 4 4 8 <=1 <=1 4 2 4 4 <=1 2
#> [16] >=16 <=1 >=16 8 <=1 2 <=1 4 4 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.125 0.125 0.5 0.125 1 0.125 0.5 2 8 8 1 8
#> [13] 4 2 0.125 0.25 1 4 0.5 0.5 8 0.25 0.25 0.125
#> [25] 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 44 35 15 34 22 8 39 24 20 46 37 46 19 49 28 29 48 50 15 35 26 8 50 33 30
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 14 14 15 13 11 17 15 12 14 16 14 15 15 12 14 14 11 15 12 14 17 14 11 12 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 15 25 23 22 24 22 16 20 22 17 24 22 27 18 19 27 20 24 15 25 24 24 20 25 23
# }