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] 0.0625 8 0.005 1 <=0.002 0.25 2 2 0.005
#> [10] 0.0625 0.025 128 32 128 4 0.25 <=0.002 0.005
#> [19] 128 <=0.002 2 <=0.002 0.025 0.0625 256
random_disk(25)
#> Class <disk>
#> [1] 30 36 49 27 28 21 45 21 47 48 20 6 47 11 47 33 26 11 48 36 23 46 8 47 33
random_rsi(25)
#> Class <rsi>
#> [1] S R S S S S S I S S R R S S S S I R I S I R R 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] 0.25 0.0625 4 8 4 0.5 64 0.002 64 2
#> [11] 0.01 >=128 64 0.25 16 0.002 0.025 0.125 64 0.01
#> [21] 0.002 16 1 4 1
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#> [1] 16 16 >=32 2 16 8 >=32 8 4 >=32 2 8 2 4 8
#> [16] 1 8 2 1 4 16 >=32 >=32 16 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#> [1] 1 <=0.125 >=8 2 1 1 4 <=0.125 1
#> [10] 0.25 <=0.125 0.25 4 0.5 0.25 0.5 0.5 2
#> [19] <=0.125 >=8 <=0.125 4 2 >=8 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#> [1] 43 23 12 45 35 12 16 32 44 17 18 47 48 25 48 17 50 22 29 35 46 50 49 24 40
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#> [1] 14 13 16 11 13 12 16 13 16 11 14 17 16 14 13 17 13 14 16 13 15 15 15 14 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#> [1] 19 21 19 26 17 25 19 27 19 23 23 22 17 23 25 19 19 25 21 18 27 18 15 18 18
# }