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 2022 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] 8 0.002 0.005 0.125 >=256 16 32 >=256 0.025 0.125 >=256 0.005
#> [13] >=256 >=256 >=256 0.025 16 1 0.125 128 8 0.001 128 0.005
#> [25] 64
random_disk(25)
#> Class 'disk'
#> [1] 49 42 10 37 12 22 29 28 11 50 44 39 14 41 6 16 47 46 43 38 24 15 42 45 38
random_sir(25)
#> Class 'sir'
#> [1] I R I S I I R I R R I R I I I S I I R I I S R R I
# \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 1 64 8 0.025 0.001 0.001 2 0.5 16 0.005 32
#> [13] 0.125 1 32 0.25 0.125 0.002 2 0.5 4 0.125 0.01 8
#> [25] 0.001
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 1 >=16 4 >=16 1 <=0.5 2 >=16 <=0.5 <=0.5 >=16
#> [13] 8 4 8 >=16 2 <=0.5 <=0.5 1 >=16 2 1 8
#> [25] 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 8 0.5 0.25 4 >=16 8 0.25
#> [9] <=0.0625 0.125 1 8 >=16 >=16 >=16 1
#> [17] 4 0.5 <=0.0625 0.5 2 2 0.125 0.5
#> [25] 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 30 23 42 49 27 45 39 9 28 12 43 30 29 49 45 25 13 46 41 47 10 26 37 14 27
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 14 16 14 14 14 17 13 15 17 13 13 15 11 13 14 13 14 12 13 11 12 15 14 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 20 21 17 20 27 17 24 17 25 27 18 27 25 16 21 25 20 19 27 15 17 20 24 20
# }