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] 0.125 64 16 128 256 0.0625 8 0.125 0.025 0.0625
#> [11] 2 16 0.002 16 0.002 64 0.25 256 0.01 256
#> [21] 2 2 0.001 8 32
random_disk(25)
#> Class <disk>
#> [1] 46 49 33 49 40 41 18 50 25 50 48 50 40 32 15 46 29 13 12 11 45 25 35 16 6
random_rsi(25)
#> Class <rsi>
#> [1] S R I I I I I I R R S S I I S S S R R S S S R S S
# \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] 0.25 <=0.001 0.0625 0.025 0.002 8 0.125 0.5 2
#> [10] 0.25 0.002 64 >=128 0.5 0.5 0.125 0.002 1
#> [19] 0.005 0.125 0.125 >=128 0.005 32 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 2 2 1 4 32 4 4 16 16 8 32 8 8 2 32 4 16 16 8 4 32 2 2 8 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 2 0.5 1 <=0.0625 <=0.0625 0.25 >=4 0.25
#> [9] >=4 0.125 2 >=4 >=4 1 0.25 >=4
#> [17] >=4 1 <=0.0625 2 <=0.0625 2 0.25 <=0.0625
#> [25] 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 49 49 35 45 22 50 22 25 39 40 19 48 29 50 46 22 46 50 17 11 35 11 26 45 24
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 11 11 13 12 11 12 15 14 12 13 15 16 15 14 12 11 12 14 12 13 15 14 14 16 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 17 19 16 17 26 19 19 19 24 26 19 21 15 21 16 27 23 16 18 26 27 16 25 15 22
# }