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] 8 64 8 0.25 8 2 0.005 16 256 32 16 0.125
#> [13] 0.125 64 32 0.25 256 4 1 0.125 32 0.5 0.025 128
#> [25] 0.25
random_disk(25)
#> Class <disk>
#> [1] 27 41 44 30 6 49 34 45 48 31 48 31 31 41 49 46 14 24 31 12 45 24 44 36 38
random_rsi(25)
#> Class <rsi>
#> [1] I I R S S R S S S I I R I R I I S R R R S I S I S
# \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] 0.125 0.25 0.125 0.002 4 2 8 32 0.0625 0.002
#> [11] 0.125 0.005 1 0.002 0.001 16 0.025 0.25 0.5 128
#> [21] 2 0.005 128 4 0.002
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] <=1 4 8 8 8 8 8 >=16 2 2 4 2 <=1 8 2
#> [16] <=1 >=16 2 2 8 4 4 8 <=1 <=1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.125 0.25 2 0.5 0.0625 8 0.25 0.25 0.125 1
#> [11] 2 0.125 0.0625 4 0.5 0.125 2 8 4 0.0625
#> [21] 0.5 0.25 0.5 8 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 42 30 13 25 19 37 49 26 38 8 46 40 23 25 44 11 40 13 22 34 15 36 47 49 49
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 15 14 17 16 15 16 15 11 16 16 15 15 13 13 15 11 15 15 15 17 13 11 15 17 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 20 25 18 16 15 19 16 21 23 19 25 18 16 16 16 18 16 27 17 27 23 22 17 19 19
# }