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] 0.01 0.025 0.005 1 0.5 0.25 0.25 <=0.001 1
#> [10] <=0.001 0.025 0.005 8 32 >=128 16 4 32
#> [19] 4 0.5 2 2 16 <=0.001 8
random_disk(25)
#> Class 'disk'
#> [1] 45 30 36 15 21 12 49 24 19 17 31 44 41 45 36 11 27 9 48 42 42 24 41 23 13
random_sir(25)
#> Class 'sir'
#> [1] I R S S S I S S S R I S S I S S R R I R S I I S R
# \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 0.01 0.01 0.002 8 0.125 0.001 0.025 1 0.001 1 0.001
#> [13] 2 32 0.5 0.005 1 2 0.125 2 4 0.25 0.005 4
#> [25] 0.01
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 2 0.5 1 0.5 16 1 32 8 0.5 16 0.5 1 32 64 32 8 1 2
#> [20] 64 8 32 16 32 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 0.5 4 2 4 4 >=16 4 2 0.25
#> [11] >=16 0.5 4 >=16 0.0625 0.125 0.25 8 0.25 1
#> [21] 2 0.25 2 2 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 24 18 17 31 47 37 24 43 10 22 43 32 37 33 26 11 19 38 43 43 41 47 34 48 11
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 16 15 15 16 12 11 16 12 17 12 16 17 11 16 11 11 15 16 16 14 16 16 12 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 23 23 17 15 15 22 19 18 20 16 27 27 20 25 15 26 17 23 24 19 16 16 22 23
# }