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] 4 0.005 4 0.005 8 0.0625 2 0.125 0.025 0.005
#> [11] 0.25 0.002 0.001 32 8 64 16 0.01 8 32
#> [21] 0.25 16 0.0625 32 >=256
random_disk(25)
#> Class 'disk'
#> [1] 42 25 50 41 34 45 37 31 14 48 43 11 44 45 22 49 42 29 36 50 31 41 49 23 41
random_sir(25)
#> Class 'sir'
#> [1] R R R S R S S R I R R R I S R I R I S I S R I R R
# \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 16 8 0.025 32 1 2 0.025 64 0.25 1 0.005
#> [13] 0.25 32 1 0.5 16 0.25 0.125 0.025 1 0.001 0.125 0.005
#> [25] 2
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=32 8 2 2 16 1 2 2 2 4 2 >=32 16 >=32 >=32
#> [16] 2 4 1 2 16 4 >=32 8 16 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 0.0625 >=16 8 2 0.0625 1 0.125 0.25 1
#> [11] 0.25 4 0.0625 0.25 1 0.0625 1 0.125 8 4
#> [21] 2 2 4 0.0625 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 38 47 47 49 23 43 41 49 31 43 26 46 49 48 49 42 40 24 44 23 50 11 42 13 33
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 16 12 13 11 17 16 11 14 17 17 16 11 15 14 16 12 15 16 14 15 13 16 14 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 27 19 22 22 27 17 19 25 25 27 16 25 24 15 24 27 25 26 21 22 23 25 23 25
# }