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] 256 1 0.001 128 0.001 64 256 0.001 0.002 16 128 256
#> [13] 0.001 64 8 0.025 2 0.002 128 64 128 0.001 0.01 0.25
#> [25] 0.025
random_disk(25)
#> Class <disk>
#> [1] 6 22 25 8 47 50 15 46 23 33 41 11 48 17 36 28 15 6 11 44 34 19 9 48 29
random_rsi(25)
#> Class <rsi>
#> [1] I R R R R R I R I R S R S S S I S S S S I R I 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] 0.025 32 0.125 32 0.0625 0.25 0.125 0.002 0.125 0.25
#> [11] 0.0625 2 2 0.01 0.5 0.001 0.025 0.25 4 0.01
#> [21] 0.0625 0.002 32 8 >=64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 2 32 8 <=1 16 8 4 32 32 8 <=1 16 8 <=1 4 8 <=1 8 16
#> [20] 16 2 4 8 32 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] <=0.0625 1 0.5 0.125 <=0.0625 0.5 4 0.5
#> [9] 4 0.25 2 2 <=0.0625 0.25 0.125 <=0.0625
#> [17] 1 1 >=8 2 0.125 4 <=0.0625 2
#> [25] 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 27 46 48 46 45 11 8 45 45 13 31 50 41 43 24 16 32 41 42 42 42 46 41 26 26
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 12 15 14 15 17 12 14 15 11 11 16 15 16 17 13 16 11 17 14 15 16 15 12 16 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 27 16 15 19 18 15 24 26 25 18 22 17 20 26 19 18 23 26 16 24 19 22 21 20 20
# }