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 0.01 64 0.005 0.125 <=0.001 0.25 128 0.025
#> [10] 0.005 1 64 0.0625 1 0.005 8 >=256 128
#> [19] 0.025 >=256 0.5 4 16 2 4
random_disk(25)
#> Class 'disk'
#> [1] 27 23 46 49 8 14 18 19 42 37 46 37 26 31 39 50 23 50 44 45 46 37 41 34 14
random_sir(25)
#> Class 'sir'
#> [1] R R R I R S S I S R I I I S S S R R R S I S 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] <=0.001 0.25 4 1 >=128 0.0625 0.01 0.002 0.025
#> [10] 0.0625 0.0625 0.25 0.125 0.25 0.01 0.025 0.125 0.0625
#> [19] <=0.001 0.002 2 32 64 32 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 16 4 2 16 32 8 8 16 >=64 >=64 4 8 16 <=1
#> [16] <=1 >=64 >=64 >=64 >=64 32 2 4 >=64 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 8 1 0.125 1 1 0.125 0.025 0.0625 0.125 8
#> [11] 0.5 0.25 0.0625 0.0625 0.125 4 0.0625 8 0.25 0.0625
#> [21] 0.125 1 8 0.25 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 43 49 26 44 44 15 26 44 43 22 42 10 37 42 48 47 13 31 48 35 32 49 34 37 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 17 16 12 17 14 13 11 15 15 12 13 16 14 11 11 15 17 16 17 17 14 13 11 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 16 21 25 21 19 15 26 27 27 26 15 27 18 19 17 25 25 26 18 24 17 21 18 16 17
# }