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] 1 256 2 0.125 64 0.5 0.025 <=0.001 0.25
#> [10] 0.025 16 0.0625 0.005 32 <=0.001 0.25 2 0.25
#> [19] 16 128 64 256 32 256 0.005
random_disk(25)
#> Class 'disk'
#> [1] 12 10 46 48 20 46 12 18 31 21 8 7 24 21 48 48 26 42 40 18 47 7 16 9 9
random_sir(25)
#> Class 'sir'
#> [1] S R I S R S I R I S R S I I S I R S S I S I R 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] 2 32 4 0.25 4 0.5 2 0.5 0.01 0.01
#> [11] 0.001 1 2 2 0.005 0.5 >=256 0.5 16 0.0625
#> [21] 0.002 0.01 0.0625 8 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 >=16 4 1 8 4 4 >=16 1 4 8 8 >=16 2 >=16
#> [16] 1 1 1 2 >=16 >=16 8 1 >=16 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 2 0.0625 0.025 1 0.025 0.125 0.025 0.125 4
#> [11] 0.5 4 0.025 4 8 2 4 0.5 0.0625 0.25
#> [21] 0.025 0.5 >=16 0.125 0.025
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 47 49 49 45 43 38 34 45 32 20 15 23 21 20 46 21 40 46 46 17 24 33 23 40 49
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 15 15 17 17 15 12 14 16 15 16 12 13 12 13 17 17 13 12 14 13 17 16 17 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 19 16 24 26 16 22 25 24 24 21 27 17 20 23 18 27 26 15 24 26 22 26 18 24
# }