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] 32 0.25 0.025 4 8 0.125 0.5 0.25 0.125 128 0.01 0.125
#> [13] 0.025 4 0.005 256 8 0.01 256 128 0.125 0.002 0.25 64
#> [25] 2
random_disk(25)
#> Class 'disk'
#> [1] 27 8 20 42 15 40 27 37 23 32 26 48 6 47 10 50 43 19 48 46 38 37 37 40 32
random_sir(25)
#> Class 'sir'
#> [1] I S R R R I I R S I S S I I I S S S S R S I R 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] 1 16 64 8 0.01 1 0.5 0.005 4 64
#> [11] 0.01 16 0.5 0.001 0.025 0.005 16 0.25 2 0.0625
#> [21] 0.001 0.005 2 0.25 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 0.5 32 1 2 <=0.25 1 1 0.5 16
#> [11] 0.5 16 1 <=0.25 8 <=0.25 1 4 2 4
#> [21] 4 0.5 0.5 32 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 2 >=4 2 1 0.25 >=4 0.25 2 0.125
#> [11] 0.125 0.5 0.0625 0.25 0.25 0.125 1 0.25 1 2
#> [21] 1 >=4 0.125 2 >=4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 17 13 10 44 40 18 34 19 15 9 17 28 12 35 47 40 49 34 23 21 31 43 34 42 19
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 15 17 12 17 15 16 13 13 12 14 16 15 17 13 15 11 15 17 14 13 11 15 15 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 23 16 16 16 24 19 18 18 18 23 22 15 17 24 22 18 15 21 23 26 23 26 20 22
# }