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] 64 0.125 0.0625 32 0.025 64 0.01 64 4 0.001
#> [11] 128 0.5 0.25 32 0.025 0.01 0.025 0.001 0.01 0.005
#> [21] 0.0625 0.01 >=256 64 64
random_disk(25)
#> Class 'disk'
#> [1] 46 32 21 18 42 16 48 9 47 35 7 21 41 23 39 12 45 27 33 31 41 25 42 47 46
random_sir(25)
#> Class 'sir'
#> [1] I I S I S S I S R R R I S R I I I R I I I R R S 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] 8 0.125 0.002 0.25 0.25 16 1 0.002 128 1 0.025 0.25
#> [13] 2 0.002 0.001 64 4 0.001 0.025 0.001 0.005 0.005 0.01 0.01
#> [25] 0.25
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 1 2 1 1 1 16 4 0.5 16 2 8 16 1 8 0.5 2 1 4
#> [20] 8 8 16 0.5 4 0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.025 <=0.025 0.0625 <=0.025 1 <=0.025 2 <=0.025 <=0.025
#> [10] 0.0625 0.125 0.0625 1 2 1 8 2 0.25
#> [19] 8 8 8 0.25 8 0.25 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 43 11 19 9 48 20 22 49 10 27 10 35 8 27 31 26 28 13 34 32 12 37 46 41 26
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 14 14 17 15 16 17 14 12 17 13 11 13 15 17 16 17 11 11 17 14 13 12 17 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 22 21 20 17 21 21 25 16 22 23 25 15 25 19 18 23 18 24 21 22 24 17 18 24
# }