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] 0.01 1 0.025 4 2 256 0.125 0.005 0.0625
#> [10] 4 0.005 64 1 16 0.5 <=0.002 0.5 0.005
#> [19] 0.005 16 16 128 0.01 16 <=0.002
random_disk(25)
#> Class <disk>
#> [1] 49 25 17 40 42 40 37 45 6 46 13 6 48 38 38 28 46 14 40 9 19 41 41 40 43
random_rsi(25)
#> Class <rsi>
#> [1] S S R R R R I S I I S R I S S R I S S R S R I R 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] 0.5 32 4 4 0.002 8 2 0.025 <=0.001
#> [10] 0.25 128 0.002 16 32 0.125 16 0.5 4
#> [19] 256 16 0.0625 <=0.001 0.5 256 32
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 8 >=16 >=16 >=16 >=16 2 <=1 8 8 4 8 <=1 4 <=1 <=1
#> [16] >=16 >=16 <=1 <=1 8 8 4 2 4 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 4 0.5 0.0625 4 >=16 1 0.5 0.5 0.0625
#> [10] 4 0.25 0.25 0.0625 8 4 8 0.25 8
#> [19] 0.25 4 1 >=16 <=0.025 4 <=0.025
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 21 37 33 13 16 25 34 10 46 40 48 31 42 13 33 30 9 24 15 41 20 22 43 45 42
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 13 17 15 16 16 11 16 14 15 13 12 13 13 14 14 16 13 16 14 17 13 15 11 17 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 18 20 17 22 27 15 22 15 18 25 20 19 22 19 15 23 15 19 27 17 23 15 16 15 21
# }