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] 2 64 16 >=256 64 128 <=0.001 0.5 8
#> [10] 16 2 8 8 2 >=256 32 64 0.5
#> [19] >=256 16 0.5 0.0625 64 0.01 0.125
random_disk(25)
#> Class <disk>
#> [1] 41 20 7 37 10 50 20 23 38 32 44 6 34 26 19 46 43 11 32 50 18 12 32 19 37
random_rsi(25)
#> Class <rsi>
#> [1] S R R R I S I S I R I I S S R R R I R R R I S R R
# \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] 8 32 8 0.005 4 8 0.025 >=64 0.5 0.001 0.025 0.001
#> [13] 0.125 >=64 0.125 0.002 0.01 16 >=64 8 >=64 0.5 0.125 32
#> [25] 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 16 4 8 4 16 8 16 <=1 4 2 4 4 4 2 8 4 <=1 16 16
#> [20] 2 <=1 <=1 4 16 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.5 0.125 0.25 0.125 0.125 0.125 4 2 0.0625 0.125
#> [11] 0.0625 2 0.5 1 1 2 2 4 1 0.125
#> [21] 2 2 1 0.25 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 26 40 17 35 19 24 48 16 44 33 47 16 49 50 37 40 41 22 29 46 47 38 22 49 30
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 16 13 14 15 14 16 17 16 14 11 16 17 12 14 14 12 11 17 13 12 12 11 14 14 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 23 23 21 23 20 23 18 20 18 27 25 17 16 26 22 20 17 20 19 23 20 24 24 18 25
# }