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] <=0.001 1 0.25 128 0.01 0.025 0.025 16 8
#> [10] 128 64 16 <=0.001 0.01 0.0625 0.0625 0.5 0.0625
#> [19] 0.025 8 128 32 0.025 0.0625 0.01
random_disk(25)
#> Class <disk>
#> [1] 30 11 11 41 49 41 47 7 44 29 15 18 25 6 30 49 24 38 15 23 15 17 43 45 6
random_rsi(25)
#> Class <rsi>
#> [1] S I I S R R I I S R S I S R R R R I S I R 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] 0.01 0.025 8 2 1 0.002 0.125 2 64 0.25 16 32
#> [13] 0.005 0.125 0.01 256 0.5 1 4 0.25 0.125 0.001 256 0.5
#> [25] 128
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 0.5 >=64 2 4 8 0.5 >=64 2 1 32
#> [11] >=64 16 8 <=0.25 <=0.25 4 <=0.25 16 16 <=0.25
#> [21] 16 32 32 <=0.25 <=0.25
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 0.25 1 >=8 <=0.125 0.25 4 0.5 >=8 >=8
#> [10] 0.25 0.25 0.25 1 4 <=0.125 1 >=8 4
#> [19] 4 0.5 2 >=8 >=8 >=8 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 19 46 14 40 42 13 26 42 12 21 41 26 21 12 24 27 40 21 45 37 24 13 41 17 41
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 17 16 17 11 13 14 13 17 17 16 17 12 17 11 16 11 13 15 13 11 16 12 14 16 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 22 17 19 18 25 20 18 23 18 15 23 20 24 23 21 20 18 21 18 21 23 15 18 25 22
# }