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] 0.002 256 256 1 4 32 0.002 256 0.5 0.001
#> [11] 2 0.5 0.002 0.25 64 0.001 8 1 0.025 1
#> [21] 0.0625 4 0.025 8 0.5
random_disk(25)
#> Class 'disk'
#> [1] 45 39 38 39 45 40 12 49 22 43 44 20 18 8 50 40 49 22 15 22 38 45 12 49 41
random_sir(25)
#> Class 'sir'
#> [1] R R S I I S R R I I R S I S I I I I I I S I S 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 0.01 0.0625 0.005 <=0.001 1 <=0.001 1 0.01
#> [10] 0.5 0.5 2 16 16 8 0.0625 32 8
#> [19] <=0.001 4 0.002 0.25 0.005 0.0625 0.025
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.5 0.25 >=32 0.25 1 4 1 16 8 8 8 0.25 1 0.25 8
#> [16] 2 2 4 8 >=32 0.25 >=32 >=32 >=32 0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 2 1 0.5 0.25 0.125 0.5 4
#> [9] 1 0.5 1 0.5 1 1 2 4
#> [17] 0.125 0.25 0.125 0.5 0.5 0.25 <=0.0625 0.5
#> [25] 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 38 43 19 13 42 30 49 18 45 41 11 27 48 9 34 45 49 48 10 11 43 11 46 47 47
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 15 16 17 11 12 15 14 14 16 15 14 15 15 14 14 12 11 12 17 14 16 12 14 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 27 20 17 17 16 23 17 15 20 25 16 16 21 26 18 22 20 24 18 26 21 20 19 18
# }