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 drug, 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_sir(size = NULL, prob_SIR = 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 drug code with
as.ab()- ...
ignored, only in place to allow future extensions
- prob_SIR
a vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value)
Details
The base R function sample() is used for generating values.
Generated values are based on the EUCAST 2022 guideline as implemented in the clinical_breakpoints 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] 0.01 0.5 0.005 8 0.0625 0.025 128 0.5 0.0625
#> [10] <=0.001 <=0.001 0.025 0.0625 32 128 0.01 2 0.01
#> [19] 0.25 >=256 0.0625 0.125 0.25 0.5 0.25
random_disk(25)
#> Class 'disk'
#> [1] 41 13 29 25 39 21 41 12 42 22 22 46 34 48 43 18 18 16 41 49 37 13 28 50 46
random_sir(25)
#> Class 'sir'
#> [1] R I S R I I R S I S R S R I S R R S R R S S R 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] 2 0.002 0.25 0.125 0.125 0.0625 16 64 8
#> [10] 32 0.25 1 0.005 0.025 128 <=0.001 0.002 <=0.001
#> [19] 0.5 2 4 8 0.0625 0.01 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 0.5 2 4 32 1 1 8 0.5 32 8 32 16 2 2 4 8 32 32
#> [20] 4 0.5 16 2 1 32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 0.5 0.5 0.125 0.125 8 0.0625 0.5 4 4
#> [11] 2 0.0625 2 0.125 0.5 1 16 0.0625 0.5 4
#> [21] 0.5 1 0.25 0.0625 4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 16 47 12 24 18 30 9 41 41 46 9 46 18 46 41 42 24 41 31 37 27 46 19 43 24
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 15 11 13 16 11 13 16 13 12 17 12 13 16 16 15 17 16 17 12 14 15 12 12 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 22 19 21 20 22 25 15 16 16 25 22 22 15 21 19 16 23 22 16 23 21 19 26 18
# }