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 0.002 4 2 0.005 0.025 >=256 128 0.002
#> [10] 2 <=0.001 2 64 16 >=256 0.125 0.002 0.002
#> [19] 0.005 0.25 0.005 2 >=256 0.01 16
random_disk(25)
#> Class <disk>
#> [1] 28 48 49 18 11 30 16 23 16 12 35 47 42 8 20 49 44 31 42 25 18 7 26 41 44
random_rsi(25)
#> Class <rsi>
#> [1] R I I R S R S S I S I I S I R I R S I R S I S S 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] 0.005 0.002 128 2 0.0625 1 <=0.001 256 16
#> [10] 32 <=0.001 <=0.001 32 128 64 64 32 0.025
#> [19] 8 2 0.002 0.5 0.125 <=0.001 256
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 4 8 2 8 8 <=0.5 2 4 <=0.5 4 32 4
#> [13] <=0.5 32 <=0.5 1 2 <=0.5 <=0.5 8 64 <=0.5 16 64
#> [25] <=0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 2 4 0.25 1 <=0.125 1 2 0.5 2
#> [10] 1 2 <=0.125 0.5 1 4 4 1 <=0.125
#> [19] 0.5 0.5 0.5 2 2 4 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 38 25 31 29 9 27 9 16 47 41 43 32 19 14 38 18 28 11 8 42 43 22 46 18 28
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 12 15 14 17 11 15 17 16 15 17 14 12 15 14 13 16 12 13 12 12 12 16 12 15 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 21 18 23 25 23 16 15 19 19 19 25 27 27 17 21 21 23 18 22 25 27 25 18 15 15
# }