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] 1 2 0.5 32 0.01 1 0.5 <=0.002 0.005
#> [10] 0.01 32 >=256 0.01 4 0.125 0.025 32 >=256
#> [19] 1 1 4 0.025 4 64 0.0625
random_disk(25)
#> Class <disk>
#> [1] 46 43 39 46 43 42 23 46 47 47 49 43 50 47 45 32 40 43 37 43 40 48 21 12 49
random_rsi(25)
#> Class <rsi>
#> [1] R S S I S R I I I R S R R R S R R S R I I I S S I
# \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] 32 0.5 0.001 16 0.001 2 0.0625 0.0625 16 0.125
#> [11] 0.025 32 0.5 0.005 16 0.125 0.0625 0.125 0.002 64
#> [21] 0.01 32 8 16 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 2 >=32 16 4 4 16 2 16 4 2 >=32 2
#> [13] 2 <=0.5 <=0.5 4 8 8 1 16 16 >=32 8 <=0.5
#> [25] 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 1 >=16 2 0.25 0.125 8 0.25 >=16 1 1 8 0.5
#> [13] 8 0.5 >=16 0.25 1 0.5 >=16 1 4 0.125 8 2
#> [25] 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 28 44 33 10 35 18 23 48 50 33 44 27 41 19 40 45 44 42 18 42 38 29 47 47 48
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 12 17 15 17 14 16 17 13 14 16 16 16 12 13 12 12 14 12 16 17 17 12 15 13 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 24 22 25 27 24 26 18 22 17 20 24 18 17 20 23 26 15 22 22 21 19 17 16 17 16
# }