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 8 0.001 0.01 0.002 0.01 4 64 0.001 1
#> [11] >=256 0.0625 64 32 2 0.01 128 0.002 0.125 4
#> [21] 4 2 128 128 128
random_disk(25)
#> Class <disk>
#> [1] 17 8 25 21 29 42 27 20 13 48 11 35 32 36 30 34 12 19 43 42 15 46 46 34 48
random_rsi(25)
#> Class <rsi>
#> [1] I S R S I S R I S R S S R R I I R R I R S I S S 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] 64 16 <=0.001 <=0.001 0.002 >=256 >=256 0.01 0.125
#> [10] 0.25 >=256 0.005 0.5 0.01 0.5 2 16 64
#> [19] 64 0.125 1 128 0.025 32 128
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] <=1 8 16 4 <=1 2 16 8 8 16 <=1 8 <=1 <=1 4 2 4 2 2
#> [20] 2 4 4 8 <=1 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.25 0.25 16 8 4 4 1 2 8 0.125 1 4
#> [13] 4 0.25 1 4 0.125 0.125 1 4 16 2 0.5 8
#> [25] 4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 17 40 22 46 19 41 16 27 42 10 39 25 10 26 12 36 50 20 33 11 49 43 21 8 20
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 16 12 13 17 17 15 17 12 15 16 17 15 17 14 14 17 15 14 13 13 15 14 14 12 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 16 21 15 19 21 19 15 18 15 19 24 16 25 16 23 17 15 21 19 19 21 23 27 21 16
# }