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 2024 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] 0.025 0.005 8 0.25 8 16 256 0.0625 128 0.01
#> [11] 64 16 0.01 32 8 8 0.25 128 0.5 64
#> [21] 0.0625 0.001 0.005 8 16
random_disk(25)
#> Class 'disk'
#> [1] 13 20 30 25 46 47 38 10 17 47 32 10 12 26 17 42 20 43 46 20 26 43 7 16 29
random_sir(25)
#> Class 'sir'
#> [1] I I I R S I I S R S S S R S I I I S R S I S I 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] 0.125 4 0.5 64 4 0.125 0.0625 0.005 2 0.25
#> [11] 0.5 128 4 16 128 16 0.002 1 1 0.25
#> [21] 2 4 0.002 0.025 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 <=0.25 1 2 1 8 2 8 1 0.5
#> [11] 2 <=0.25 2 <=0.25 4 0.5 4 <=0.25 1 8
#> [21] 1 16 8 8 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 0.125 <=0.0625 0.5 1 1 1 0.5
#> [9] 0.5 <=0.0625 0.125 0.5 0.25 1 0.25 4
#> [17] 8 0.125 0.125 <=0.0625 0.5 8 4 1
#> [25] >=16
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 30 29 50 11 24 10 19 24 15 15 38 13 45 46 48 40 50 40 44 36 40 26 15 36 45
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 12 13 15 11 15 14 12 12 12 11 11 17 13 14 17 15 12 13 16 14 17 16 11 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 26 16 18 17 26 21 21 21 16 20 21 26 24 23 20 20 18 17 17 18 25 24 22 24
# }