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] 0.005 0.001 0.005 >=256 64 0.25 16 32 32 8 2 0.5
#> [13] 0.5 >=256 0.005 64 0.01 1 0.005 0.125 64 0.002 0.002 8
#> [25] 8
random_disk(25)
#> Class 'disk'
#> [1] 12 8 42 46 19 36 43 46 8 35 8 50 40 40 12 42 44 42 42 32 41 45 48 44 44
random_sir(25)
#> Class 'sir'
#> [1] R I S S I R R I I I R S I S R R S I R S R 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] 0.025 2 <=0.001 0.25 2 <=0.001 0.0625 64 32
#> [10] 0.0625 2 16 0.25 0.125 16 1 0.01 2
#> [19] 0.25 2 2 32 0.125 16 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 32 32 0.5 0.25 2 16 1 8 16 8 0.5 16 32 8
#> [16] 8 8 2 4 32 4 0.5 16 2 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 8 <=0.0625 0.125 8 2 0.125 4
#> [9] 4 0.25 0.5 0.125 0.125 2 <=0.0625 0.25
#> [17] 0.25 0.5 8 0.5 0.25 8 4 4
#> [25] 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 18 14 20 11 18 35 34 48 46 34 47 41 22 14 40 32 8 43 44 10 50 43 23 19 45
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 14 17 13 17 11 15 14 11 13 17 15 11 12 13 13 17 16 14 13 13 15 17 14 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 26 25 23 19 15 24 18 24 18 25 25 25 26 19 26 18 16 26 23 20 20 16 21 23
# }