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] 64 0.025 0.01 <=0.001 16 64 0.025 0.125 1
#> [10] 0.025 16 0.5 >=256 2 64 32 4 0.005
#> [19] 0.125 128 0.5 8 0.25 0.002 0.005
random_disk(25)
#> Class 'disk'
#> [1] 20 15 10 41 49 47 42 39 8 46 10 7 17 10 27 22 27 23 11 9 36 14 29 26 16
random_sir(25)
#> Class 'sir'
#> [1] S I R I S I S R R I I I S I I R S I R R R R S 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] 0.125 0.005 0.25 0.0625 0.001 0.5 16 0.25 0.0625 0.001
#> [11] 0.001 0.001 0.25 2 0.0625 32 4 0.125 0.0625 64
#> [21] 32 >=128 0.125 0.0625 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=16 >=16 1 >=16 2 1 1 1 1 2 8 >=16 2 8 2
#> [16] 2 4 8 >=16 8 2 4 8 2 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 1 0.25 1 2 2 4 0.0625 0.5 0.0625
#> [11] 2 0.25 0.25 4 1 0.125 1 0.0625 0.125 0.0625
#> [21] 2 0.5 0.0625 0.5 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 12 17 49 8 49 22 13 47 28 44 43 20 23 45 41 39 50 30 45 48 16 15 40 34 47
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 17 11 16 12 15 16 16 16 13 12 11 12 16 15 14 16 12 15 13 11 11 17 14 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 17 24 23 17 20 20 19 22 24 25 20 23 21 21 24 18 21 24 17 21 27 21 16 16
# }