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 2023 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] 16 64 256 0.002 1 0.001 64 0.25 1 16
#> [11] 0.5 8 8 0.0625 1 0.5 0.025 256 256 1
#> [21] 0.01 1 64 32 4
random_disk(25)
#> Class 'disk'
#> [1] 49 47 14 33 49 43 41 41 43 31 20 43 42 11 18 42 8 42 16 25 42 8 15 30 29
random_sir(25)
#> Class 'sir'
#> [1] I S S I S I I S R S S I I S S I I S I R S S R I 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] 64 0.025 2 0.25 32 64 0.002 32 0.01 0.001
#> [11] 0.25 0.125 0.0625 64 128 0.002 128 128 1 0.002
#> [21] 1 0.005 0.001 4 0.001
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 1 2 1 >=16 8 1 >=16 >=16 2 1 2 1 1 8 4
#> [16] 1 1 4 2 >=16 >=16 2 4 2 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 0.25 >=8 >=8 0.5 1 1 0.125 0.25 1 2 1
#> [13] 0.25 >=8 0.25 2 1 1 >=8 0.125 0.5 >=8 0.125 0.25
#> [25] 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 45 49 24 46 23 18 15 17 17 28 40 20 21 43 39 9 33 17 8 20 30 21 44 48 41
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 15 11 14 16 16 11 15 11 17 14 15 17 17 16 16 16 12 14 12 15 13 13 13 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 23 19 19 23 15 23 18 21 24 22 25 19 19 16 17 17 16 27 21 27 25 15 21 27
# }