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] 32 0.01 0.005 0.5 0.025 >=256 0.0625 >=256 >=256
#> [10] 0.25 64 <=0.002 0.025 0.125 128 0.01 0.25 0.25
#> [19] 1 128 128 0.005 32 0.0625 2
random_disk(25)
#> Class 'disk'
#> [1] 19 15 43 41 37 41 46 47 49 9 30 39 8 36 8 19 24 14 25 48 39 7 12 8 49
random_sir(25)
#> Class 'sir'
#> [1] I S I R R R R R S R S S I R S S R S I S R S S R 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] 0.001 8 1 0.01 0.025 8 64 0.5 0.01 0.002 32 16
#> [13] 128 0.25 4 0.005 0.025 0.125 256 64 128 32 16 8
#> [25] 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 1 0.25 2 32 8 32 16 >=64 0.25 >=64 0.5 2 >=64 16
#> [16] 0.25 8 8 4 >=64 0.25 2 1 16 0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 8 1 <=0.0625 0.25 >=16 0.5 1 1
#> [9] 8 0.5 >=16 1 8 0.5 0.25 4
#> [17] <=0.0625 4 8 8 2 0.5 1 0.5
#> [25] 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 22 42 48 44 25 31 46 49 21 30 49 22 46 44 21 20 47 33 47 44 45 13 17 24 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 17 17 15 16 11 13 11 11 14 14 14 15 15 13 15 17 12 12 17 15 16 17 14 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 19 24 15 18 17 26 18 19 27 27 19 26 25 25 26 24 27 21 15 15 24 16 18 18 20
# }