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 >=256 >=256 0.5 0.25 8 0.002 0.005 4
#> [10] 4 0.125 32 0.002 0.25 0.005 0.025 128 <=0.001
#> [19] 0.01 8 128 16 0.002 1 0.025
random_disk(25)
#> Class 'disk'
#> [1] 34 27 17 6 44 17 49 39 32 27 49 45 15 40 29 29 26 10 26 50 23 10 32 33 6
random_sir(25)
#> Class 'sir'
#> [1] I R S S I I S S S I R S R R R R I S R R S S 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] 0.005 128 0.01 <=0.001 128 16 16 0.5 0.25
#> [10] 8 2 <=0.001 16 128 <=0.001 64 0.0625 0.25
#> [19] 16 128 4 <=0.001 0.125 0.01 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 16 8 4 <=1 8 8 4 4 2 2 <=1 16 4 2 8 2 2 8
#> [20] 2 8 8 16 2 <=1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.125 2 0.5 2 >=4 2 >=4 2 <=0.125
#> [10] <=0.125 0.25 >=4 <=0.125 0.5 >=4 1 1 1
#> [19] <=0.125 <=0.125 2 1 2 <=0.125 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 35 25 44 48 10 20 33 12 47 28 19 41 45 26 36 38 31 37 50 8 39 46 43 14 41
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 11 14 13 15 16 14 12 14 13 11 11 14 13 17 17 11 12 17 14 16 16 15 12 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 20 26 16 17 20 22 26 15 18 25 27 27 24 26 18 19 24 23 26 19 20 17 20 27
# }