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] 0.25 0.025 2 32 128 32 0.5 2 32
#> [10] 0.002 0.005 <=0.001 >=256 2 128 0.5 <=0.001 8
#> [19] 128 0.125 0.125 2 8 1 8
random_disk(25)
#> Class <disk>
#> [1] 45 21 42 40 33 36 34 29 9 20 43 34 40 49 28 43 44 37 43 20 35 16 11 47 15
random_rsi(25)
#> Class <rsi>
#> [1] R R S S I I S R R S R S S R R I I S S R I I S I 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] 2 2 0.0625 0.005 >=128 0.005 2 0.005 0.0625 1
#> [11] 0.001 0.01 0.5 0.001 8 0.001 16 16 16 0.01
#> [21] 8 1 32 64 8
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 1 0.5 2 <=0.25 1 8 8 0.5 2 1
#> [11] 2 2 8 4 >=16 >=16 1 <=0.25 4 0.5
#> [21] 8 0.5 >=16 8 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.0625 1 0.125 0.125 0.125 >=4 0.5 0.125 1 0.125
#> [11] 2 2 >=4 >=4 0.25 2 >=4 0.0625 1 2
#> [21] 0.0625 1 0.5 1 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 23 14 32 50 15 38 35 50 21 34 41 36 46 49 43 41 9 20 20 27 31 21 13 46 22
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 15 13 11 14 12 14 15 15 17 14 17 13 11 16 17 12 14 17 17 17 12 14 13 15 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 22 23 20 22 18 23 21 16 20 23 23 19 15 26 27 20 22 19 22 16 21 20 15 19 26
# }