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] 0.0625 0.5 4 16 4 0.0625 8 0.002 4
#> [10] 0.25 64 64 0.5 <=0.001 0.5 <=0.001 8 1
#> [19] 2 0.01 0.5 0.0625 0.125 >=256 0.025
random_disk(25)
#> Class <disk>
#> [1] 39 16 46 31 49 28 18 41 45 40 42 49 22 47 40 6 49 25 12 43 43 36 7 16 10
random_rsi(25)
#> Class <rsi>
#> [1] S I S S R S S I S R R S S S S R S R I R R R R S 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 0.002 <=0.001 0.005 0.125 256 4 32 0.01
#> [10] <=0.001 0.25 1 0.025 0.125 32 32 16 0.005
#> [19] 0.5 <=0.001 0.0625 0.5 256 2 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 32 <=0.25 16 0.5 8 <=0.25 8 16 8 32
#> [11] 32 0.5 <=0.25 32 32 32 0.5 4 8 16
#> [21] <=0.25 32 16 16 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.25 0.25 <=0.025 >=16 0.0625 0.5 8 0.25 0.25
#> [10] 4 0.125 1 0.5 0.125 8 >=16 0.0625 2
#> [19] 0.25 >=16 2 >=16 1 1 4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 47 15 40 39 45 10 36 40 47 22 12 11 44 14 45 21 17 49 24 14 11 22 44 45 11
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 16 14 13 11 11 14 12 14 15 14 14 16 15 11 14 12 13 17 11 17 13 11 15 11 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 17 25 23 21 19 21 15 15 25 22 22 16 16 18 16 25 23 24 17 23 15 25 22 23 16
# }