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 0.01 <=0.001 0.0625 0.002 0.002 2 32 2
#> [10] <=0.001 0.002 0.125 16 8 <=0.001 0.002 >=64 0.0625
#> [19] 8 0.005 0.005 0.25 0.125 2 <=0.001
random_disk(25)
#> Class <disk>
#> [1] 25 38 46 47 12 49 31 7 28 47 28 22 49 26 50 7 18 48 32 35 20 41 47 49 32
random_rsi(25)
#> Class <rsi>
#> [1] I R S I I S R R R I R S S I R R S R I R S R 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] 0.025 4 1 64 0.125 8 1 32 0.002
#> [10] 0.002 32 2 0.0625 2 0.125 <=0.001 0.25 0.002
#> [19] 128 32 0.005 8 16 64 0.025
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 2 1 8 1 >=32 >=32 <=0.5 2 16 2 4 <=0.5
#> [13] 16 4 >=32 16 4 8 8 4 >=32 2 16 16
#> [25] 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] >=16 >=16 >=16 0.5 4 1 1 1 0.25
#> [10] <=0.125 1 8 <=0.125 0.25 >=16 4 0.25 >=16
#> [19] 0.5 4 2 0.25 8 2 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 50 11 47 9 25 21 25 20 11 21 22 48 23 24 37 32 17 9 48 36 20 26 29 31 19
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 13 13 11 11 11 12 15 16 11 14 11 16 15 17 12 11 15 15 13 17 16 15 14 13 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 21 15 21 21 27 25 24 26 20 22 26 15 24 23 26 24 18 23 18 23 25 24 23 19 15
# }