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] 4 16 1 128 16 32 0.005 8 4 0.005 0.5 8
#> [13] 0.025 0.25 0.005 32 32 0.002 128 0.01 1 128 1 4
#> [25] 0.125
random_disk(25)
#> Class <disk>
#> [1] 48 40 19 20 43 37 35 37 8 6 21 40 21 32 26 45 11 32 29 23 37 27 28 25 42
random_rsi(25)
#> Class <rsi>
#> [1] R I I I R R R R S R S R S R R S R I R R R I I 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] 0.125 >=128 0.01 0.0625 0.125 1 64 0.0625 16 4
#> [11] 2 0.5 0.025 0.01 0.0625 0.5 64 32 8 0.5
#> [21] 16 16 64 32 0.25
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 2 >=32 >=32 8 4 >=32 >=32 16 4 <=1 16 4 >=32 >=32 16
#> [16] 2 >=32 8 2 4 2 >=32 2 16 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] <=0.025 1 0.25 1 0.125 0.25 <=0.025 1 8
#> [10] 1 0.0625 0.125 4 1 0.25 4 4 0.25
#> [19] 16 0.5 0.0625 0.5 16 16 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 48 35 40 32 18 32 38 50 20 46 48 40 11 24 27 46 14 41 38 24 13 19 17 45 10
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 14 16 17 14 17 13 15 14 17 13 13 11 11 11 15 12 15 14 14 17 14 13 17 16 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 23 27 17 16 26 20 21 22 18 23 27 23 27 17 16 25 25 17 21 17 17 17 22 16 27
# }