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] 64 1 4 0.025 0.01 0.5 0.25 2 >=256 1
#> [11] 1 8 8 64 0.0625 0.005 0.125 2 0.001 1
#> [21] 0.005 0.005 32 128 8
random_disk(25)
#> Class 'disk'
#> [1] 10 21 50 40 30 50 48 27 34 18 41 40 11 43 28 31 8 27 48 43 23 22 42 39 23
random_sir(25)
#> Class 'sir'
#> [1] R S S R S I I R S I R S I I I S R I S S S S I S 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] 0.025 0.001 16 32 16 0.0625 0.0625 8 256 128
#> [11] 0.01 0.5 128 0.005 8 16 32 0.0625 0.002 2
#> [21] 0.01 2 0.025 2 256
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=1 4 <=1 16 2 <=1 4 2 4 2 4 32 4 2 4 2 16 2 16
#> [20] <=1 <=1 32 2 <=1 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 0.125 8 1 4 0.125 0.125 0.5 2 0.5 8 2
#> [13] 1 0.25 0.125 0.125 1 2 0.5 8 8 4 1 0.125
#> [25] 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 40 36 14 10 48 38 42 9 50 22 15 43 22 32 19 41 10 30 22 48 45 50 35 38 43
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 11 12 11 17 17 15 12 16 12 11 11 15 14 13 13 11 15 12 11 13 14 17 14 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 20 16 25 17 20 20 23 17 27 25 16 20 24 16 21 22 24 21 26 23 21 25 15 24 21
# }