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 0.0625 0.002 >=256 4 16 4 >=256 0.01
#> [10] 8 8 4 0.0625 8 0.25 0.002 0.002 0.25
#> [19] 0.0625 >=256 <=0.001 0.025 8 0.002 128
random_disk(25)
#> Class <disk>
#> [1] 40 43 40 50 12 30 46 29 23 39 31 20 33 50 33 41 13 47 40 40 10 29 50 41 47
random_rsi(25)
#> Class <rsi>
#> [1] S R R I R R R S R S S S I I I I S S R R I S S 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 8 0.001 1 64 0.005 128 64 0.025 0.002
#> [11] 128 0.25 0.025 16 0.025 32 32 2 0.0625 >=256
#> [21] 0.001 0.005 0.005 16 8
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] >=16 4 2 2 8 1 1 0.5 4 2 0.5 1 1 >=16 2
#> [16] >=16 8 0.5 8 2 4 4 8 2 >=16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 4 0.0625 1 1 4 1 0.25 0.0625 0.5
#> [10] 2 0.5 1 <=0.025 4 0.5 0.0625 0.0625 0.25
#> [19] >=8 0.25 0.25 0.25 0.25 0.0625 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 35 47 16 42 50 35 8 11 43 46 31 23 14 35 40 46 10 28 12 47 25 42 23 22 8
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 14 11 14 13 17 16 14 16 14 11 14 15 17 16 13 14 12 11 13 16 15 13 11 13 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 15 27 24 16 20 23 20 24 18 23 26 25 22 17 25 19 19 25 18 24 21 27 22 22 23
# }