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] 0.001 0.005 0.0625 0.001 0.001 2 >=256 128 0.005 0.002
#> [11] 1 0.002 32 16 64 0.005 0.005 0.025 32 0.5
#> [21] 0.25 0.005 8 >=256 0.01
random_disk(25)
#> Class 'disk'
#> [1] 16 6 43 36 43 50 45 43 25 34 37 9 25 46 39 40 45 47 17 9 22 45 14 47 41
random_sir(25)
#> Class 'sir'
#> [1] S S S R R I S R S S I S R S R I I R I I R I S 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 0.01 >=256 0.25 0.25 1 0.002 0.25 2 0.005 0.001
#> [13] 64 0.001 0.025 0.025 64 128 0.5 16 2 0.001 0.125 8
#> [25] 0.025
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] >=32 16 8 2 8 8 1 1 8 >=32 16 <=0.5
#> [13] 2 >=32 4 >=32 >=32 >=32 4 8 2 16 4 >=32
#> [25] 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 0.125 0.125 0.25 1 1 0.0625 0.5 1 0.5
#> [11] 4 0.125 0.25 0.25 0.0625 4 0.25 0.125 4 1
#> [21] 4 0.5 0.0625 4 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 47 49 10 40 23 16 20 34 45 8 42 10 20 11 30 36 40 35 14 24 8 38 10 10 15
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 12 14 11 13 15 13 11 17 15 14 13 11 15 17 14 16 17 17 17 11 12 12 12 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 15 17 23 23 18 18 17 15 18 27 15 25 16 21 15 24 23 22 22 15 23 25 23 24
# }