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 8 0.002 0.005 0.25 >=256 0.01 0.002 64
#> [10] 0.5 4 32 0.002 16 >=256 0.01 0.002 0.0625
#> [19] 0.002 64 8 8 2 <=0.001 0.125
random_disk(25)
#> Class 'disk'
#> [1] 43 7 48 40 19 50 50 20 44 14 16 33 31 17 30 6 38 7 6 12 16 11 43 43 45
random_sir(25)
#> Class 'sir'
#> [1] R S R R S S R I S R S S R I I R S I R R R R I 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] 0.025 0.25 16 8 0.001 4 16 0.025 0.25 8
#> [11] 0.5 0.005 0.0625 2 0.125 0.002 1 16 16 0.005
#> [21] 0.001 >=32 0.002 0.0625 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 8 2 8 8 16 8 8 1 0.5 1 >=32 2 4 1
#> [16] >=32 4 2 4 4 2 16 4 16 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.0625 <=0.0625 <=0.0625 0.5 0.125 0.25 0.5 2
#> [9] 0.125 0.125 0.5 4 <=0.0625 2 0.25 4
#> [17] 2 0.25 1 2 2 <=0.0625 2 <=0.0625
#> [25] 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 30 43 22 49 40 8 14 36 49 23 12 9 17 25 43 46 30 49 34 22 50 24 39 38 46
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 15 16 14 17 14 12 13 13 17 17 12 14 16 15 14 16 14 16 13 11 16 17 13 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 22 21 23 19 20 21 25 20 19 21 19 27 22 26 25 27 21 17 26 18 23 23 26 27
# }