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 2023 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 0.125 2 0.001 16 >=128 2 32 64 2 0.5 0.5
#> [13] 1 8 0.002 0.25 64 2 32 0.002 0.25 0.025 0.5 16
#> [25] 16
random_disk(25)
#> Class 'disk'
#> [1] 37 43 42 43 44 38 14 25 37 9 10 49 34 17 50 43 9 19 45 42 18 17 43 26 31
random_sir(25)
#> Class 'sir'
#> [1] S I S I S S I S R S S I S S R I R S R I S I 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] 1 32 2 64 0.5 0.025 32 0.01 64
#> [10] 8 0.002 0.5 0.01 0.01 <=0.001 0.125 8 16
#> [19] 0.025 16 4 32 0.01 0.25 0.25
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 1 1 8 >=16 4 4 8 1 4 8 1 >=16 2 4 4
#> [16] >=16 8 8 >=16 2 4 2 4 8 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 2 0.5 1 0.125 4 0.25 4 4 0.5 0.25 4
#> [13] 8 0.25 0.5 0.125 8 4 0.5 0.125 0.125 2 0.25 0.5
#> [25] 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 17 11 43 16 49 47 41 41 23 28 26 35 44 19 50 43 36 20 45 46 14 50 40 8 17
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 14 14 13 14 11 11 17 16 15 13 14 11 16 11 13 12 13 17 16 17 12 17 11 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 26 27 21 18 19 22 19 19 15 23 23 24 19 17 19 20 21 19 21 22 23 16 19 23
# }