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] 2 4 64 0.5 2 0.025 0.25 8 0.0625 0.001
#> [11] 0.5 32 1 0.25 0.25 0.125 0.025 >=128 32 0.0625
#> [21] 0.125 32 16 8 >=128
random_disk(25)
#> Class 'disk'
#> [1] 9 12 29 26 27 48 37 36 32 47 34 44 20 36 38 12 50 48 16 34 50 34 42 44 29
random_sir(25)
#> Class 'sir'
#> [1] R R R I S I R I S I R I S I I S I S S R R S I R 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] 0.5 256 32 0.5 0.125 4 0.25 0.002 0.01 0.005
#> [11] 1 0.005 16 32 0.0625 0.0625 0.125 1 4 128
#> [21] 8 128 4 2 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 16 8 4 32 32 4 2 16 32 8 4 4 2 4 16 2 4 8
#> [20] 4 4 32 <=1 16 <=1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 1 4 0.25 0.0625 4 0.125 0.125 1 0.25 0.125
#> [11] 0.125 1 0.0625 0.125 8 4 0.5 2 0.5 0.125
#> [21] 4 0.25 0.5 0.5 4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 10 48 23 44 36 40 20 21 39 13 43 50 24 24 41 18 22 37 40 22 45 29 13 44 13
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 15 12 16 13 15 12 13 16 17 14 14 14 12 15 13 14 12 17 13 13 16 11 11 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 16 27 21 20 16 17 19 26 25 25 18 21 18 16 24 27 24 23 24 16 15 22 24 24 15
# }