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] 2 16 >=256 2 0.5 0.01 0.5 16 1
#> [10] <=0.001 1 <=0.001 >=256 2 0.5 >=256 0.002 0.5
#> [19] 128 <=0.001 0.01 64 128 16 0.125
random_disk(25)
#> Class <disk>
#> [1] 17 44 7 48 45 20 42 10 37 32 44 27 23 36 11 29 11 21 32 38 19 34 18 10 14
random_rsi(25)
#> Class <rsi>
#> [1] I S R S R I I S I S I R S R I S I R R I S I 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] 0.005 0.001 0.002 1 0.5 >=128 0.01 0.002 0.5 0.005
#> [11] 64 0.001 0.0625 0.125 1 0.0625 0.001 0.5 0.5 32
#> [21] 0.002 8 32 4 8
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] >=16 0.25 4 4 8 8 >=16 0.5 2 0.25 2 1 >=16 2 0.25
#> [16] 0.25 0.5 1 0.5 0.25 0.25 2 1 1 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 4 0.0625 4 1 16 8 4 1 1 1
#> [11] 0.5 2 1 2 1 4 0.5 1 2 0.0625
#> [21] 0.125 1 0.0625 16 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 14 20 12 27 44 48 50 12 30 17 17 41 35 27 46 44 39 9 46 40 14 47 32 23 27
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 15 12 16 16 16 12 12 16 12 14 14 11 17 13 13 17 12 16 15 15 13 11 14 16 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 23 15 25 24 25 27 22 23 18 24 17 18 19 25 25 15 23 15 25 19 25 26 23 26 23
# }