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] 16 16 0.002 0.5 1 64 <=0.001 <=0.001 0.002
#> [10] 2 2 2 0.125 256 64 0.25 2 0.002
#> [19] 128 8 0.005 64 2 0.25 64
random_disk(25)
#> Class <disk>
#> [1] 45 45 20 40 38 9 10 41 14 50 14 46 39 14 36 36 43 47 21 44 28 23 46 41 36
random_rsi(25)
#> Class <rsi>
#> [1] I R I R I R I S S I I R S S R I R S S R R R R 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] 0.025 0.25 0.5 0.0625 0.25 0.025 0.005 32 0.025
#> [10] 1 0.01 16 64 0.005 0.0625 128 1 0.01
#> [19] 0.25 <=0.001 32 0.125 0.01 0.5 2
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 2 8 >=64 0.25 >=64 2 >=64 2 2 4 8 32 32 0.5 0.5
#> [16] 2 16 32 >=64 2 16 16 4 0.25 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.0625 2 0.5 0.125 4 0.0625 2 4 1 0.0625
#> [11] 0.125 0.0625 4 0.0625 1 4 2 4 0.5 0.0625
#> [21] 0.5 1 4 0.5 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 41 26 42 45 34 45 19 24 36 47 20 50 30 33 25 50 28 45 20 34 48 32 33 38 34
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 17 14 13 17 13 17 14 12 15 17 11 11 17 15 12 13 15 15 11 13 12 17 15 12 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 22 20 25 25 25 20 23 20 18 17 16 22 15 15 18 25 25 21 15 23 24 26 19 21 17
# }