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] 0.002 64 128 2 4 0.25 0.5 0.025 >=256 0.002
#> [11] 0.0625 0.025 0.0625 32 4 0.025 0.0625 8 >=256 1
#> [21] 0.002 0.025 0.001 0.01 0.0625
random_disk(25)
#> Class <disk>
#> [1] 13 15 24 27 29 12 46 43 15 28 20 31 25 17 13 39 19 35 49 14 40 29 45 28 38
random_rsi(25)
#> Class <rsi>
#> [1] S S S S I I S S R S I I I I I S R S I R I I I 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] 4 0.125 64 16 0.01 1 64 64 8 0.25
#> [11] 1 64 64 1 0.025 0.001 0.025 0.25 1 64
#> [21] 0.125 >=256 64 0.0625 >=256
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] >=16 1 0.5 2 2 8 2 2 8 0.5 4 >=16 0.5 2 2
#> [16] 2 1 2 2 >=16 >=16 4 0.5 2 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.25 1 0.25 16 4 16 8 8 0.5
#> [10] 1 0.25 2 16 0.5 <=0.125 16 8 0.5
#> [19] 1 <=0.125 0.25 1 0.5 8 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 25 41 23 39 8 23 20 8 41 21 18 47 18 40 23 36 42 23 30 45 23 43 8 39 45
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 15 14 11 16 16 16 14 12 12 17 17 12 13 15 11 13 15 14 17 15 13 16 11 12 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 18 23 17 23 22 27 15 21 15 17 25 25 22 25 21 15 18 19 17 18 18 17 19 17 18
# }