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] 4 0.005 0.025 64 1 2 0.005 64 0.002
#> [10] 0.0625 <=0.001 0.25 0.025 16 16 32 0.125 8
#> [19] 0.125 <=0.001 0.005 0.002 8 2 64
random_disk(25)
#> Class 'disk'
#> [1] 46 9 26 16 29 29 48 9 13 22 33 6 22 8 37 44 45 49 21 37 10 42 41 33 44
random_sir(25)
#> Class 'sir'
#> [1] S S S S R I S S R S S S I I S R S R R S I R S I 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] 0.25 256 0.0625 0.025 16 0.5 0.125 128 0.01
#> [10] 1 2 1 0.005 8 256 4 0.5 0.005
#> [19] 256 0.0625 8 <=0.001 0.5 128 0.025
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 32 32 0.25 8 2 >=64 16 4 >=64 >=64 0.5 1 >=64 8
#> [16] 32 0.25 2 0.25 8 4 8 8 0.25 0.25
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 0.25 2 1 0.0625 4 2 1 4 8
#> [11] 4 4 0.25 1 0.5 1 4 0.125 8 4
#> [21] 1 0.5 0.125 0.125 4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 49 10 26 27 49 50 31 18 15 47 43 44 22 22 33 39 43 32 10 22 32 31 41 47 16
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 12 16 11 15 16 14 16 17 16 13 13 16 15 13 15 13 12 12 14 15 16 11 17 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 23 17 19 23 16 27 22 26 15 26 23 19 27 21 21 16 22 19 24 18 15 15 21 25 15
# }