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] 1 0.005 4 16 0.01 1 16 0.25 0.005
#> [10] 0.125 <=0.002 0.125 64 0.25 4 1 128 8
#> [19] 64 >=256 0.25 8 >=256 2 16
random_disk(25)
#> Class 'disk'
#> [1] 32 30 15 34 20 43 17 28 30 50 25 10 47 23 26 13 32 24 28 46 36 14 50 46 21
random_sir(25)
#> Class 'sir'
#> [1] S R S R I R S S S I S I R I I I S I R I S S 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] 2 >=64 0.025 16 0.125 2 32 32 16
#> [10] 0.5 2 0.0625 16 0.25 0.01 4 0.002 16
#> [19] 1 <=0.001 0.0625 0.0625 8 >=64 2
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 1 4 2 1 1 >=16 0.5 4 0.5 0.5 1 2 >=16 2
#> [16] 4 0.5 8 2 >=16 0.5 4 8 2 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] >=4 0.25 0.5 0.5 0.125 1 0.25 >=4 0.5 2
#> [11] 0.5 1 0.0625 0.5 0.5 0.0625 2 0.125 1 1
#> [21] 0.25 0.0625 1 0.25 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 16 33 30 28 41 44 12 12 40 23 45 9 40 49 34 33 20 10 16 42 39 8 40 24 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 13 17 11 14 12 13 13 13 11 15 13 15 15 11 13 14 12 13 12 17 16 15 14 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 20 22 21 24 15 15 22 26 15 27 21 15 15 22 19 20 20 27 24 18 15 26 25 15
# }