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] 0.005 0.002 0.025 128 1 0.002 0.0625 0.25 8
#> [10] 64 2 0.5 0.0625 128 128 >=256 32 0.01
#> [19] 4 0.002 32 8 8 8 <=0.001
random_disk(25)
#> Class <disk>
#> [1] 35 28 42 31 7 47 45 37 17 44 17 26 25 47 40 22 10 32 36 50 50 24 46 40 10
random_rsi(25)
#> Class <rsi>
#> [1] R I S R I R R S S S S I S I I R I I I S I I I 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] 0.01 0.0625 0.25 0.001 8 0.0625 32 8 0.001 1
#> [11] 32 >=64 >=64 8 32 0.0625 0.125 0.5 0.25 0.002
#> [21] 1 1 0.5 16 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 64 1 8 16 16 16 8 64 16 32 1 64 8 16 2 2 32 32 32 4 32 1 8 2 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.0625 1 4 2 1 0.0625 0.025 0.025 0.125 2
#> [11] 4 0.025 0.25 0.25 0.025 0.25 1 2 0.25 0.5
#> [21] 4 1 1 0.025 4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 8 24 37 27 23 31 14 9 18 27 42 22 44 41 22 24 22 42 25 49 27 30 30 8 46
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 12 13 14 12 12 13 14 12 16 13 14 15 11 16 17 12 12 17 11 13 15 11 13 17 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 24 26 22 26 25 20 24 22 26 20 19 20 27 19 15 15 17 15 22 27 18 15 27 16 25
# }