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] 0.025 128 >=256 0.025 4 0.01 4 0.0625 16
#> [10] <=0.002 64 32 128 64 >=256 16 32 0.005
#> [19] 1 8 8 1 <=0.002 32 0.025
random_disk(25)
#> Class 'disk'
#> [1] 30 34 33 48 14 38 44 16 49 44 48 15 38 11 44 18 11 45 48 36 39 44 45 38 45
random_sir(25)
#> Class 'sir'
#> [1] S R I R S I R I S R I R S I S S S R S S R S R S R
# \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 >=128 1 64 64 >=128 64 2 0.025 0.001
#> [11] 0.0625 0.25 0.01 0.002 0.025 0.001 0.005 0.025 32 64
#> [21] 0.005 0.25 4 0.001 2
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 64 8 16 8 8 2 <=1 16 32 2 32 64 64 2 8 8 <=1 16 <=1
#> [20] 8 <=1 64 16 64 32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.0625 >=4 2 <=0.0625 1 0.25 0.25 2
#> [9] 0.5 >=4 >=4 >=4 1 >=4 1 1
#> [17] 0.25 >=4 0.25 0.25 >=4 1 2 0.125
#> [25] 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 28 35 37 15 14 27 50 33 48 14 16 8 10 49 46 24 44 46 19 36 40 33 38 48 27
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 11 14 11 13 14 16 17 11 16 16 14 13 12 12 16 13 12 14 15 15 15 16 11 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 19 17 17 18 23 25 27 24 20 21 21 15 25 24 26 22 26 24 21 19 16 27 21 26
# }