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] 64 2 0.002 128 2 2 0.005 0.005 256
#> [10] 2 0.025 128 256 0.5 1 256 <=0.001 0.025
#> [19] 0.002 0.0625 8 2 128 32 0.5
random_disk(25)
#> Class <disk>
#> [1] 41 50 44 50 41 22 8 38 35 50 20 13 9 6 17 45 34 12 45 39 44 39 15 35 12
random_rsi(25)
#> Class <rsi>
#> [1] R R S I R I S I S I I S R S S I R S S I I S S I 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] 0.002 32 <=0.001 1 0.125 0.0625 0.002 0.002 0.01
#> [10] 0.002 64 32 0.5 0.5 2 4 32 0.0625
#> [19] 0.005 0.025 0.002 32 >=128 0.005 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 8 1 16 32 <=0.25 <=0.25 0.5 16 2 <=0.25
#> [11] 4 <=0.25 32 4 1 <=0.25 32 4 16 16
#> [21] 1 1 8 1 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 2 8 8 1 0.125 8 4 0.5 0.125 >=16 0.025 >=16
#> [13] 2 >=16 0.5 0.025 1 8 4 0.125 8 1 2 4
#> [25] >=16
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 43 45 38 25 41 41 36 22 23 44 50 50 10 33 43 40 23 46 19 23 39 14 8 43 27
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 17 13 13 12 17 13 17 11 13 17 14 11 14 15 11 16 13 17 11 16 11 12 14 15 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 15 17 20 25 19 17 25 18 23 20 17 17 19 26 19 21 26 16 20 18 16 15 18 15 18
# }