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] 1 128 0.01 0.25 256 0.002 <=0.001 0.025 0.005
#> [10] 2 256 0.01 4 8 64 4 0.002 0.01
#> [19] 0.0625 128 0.025 2 1 <=0.001 <=0.001
random_disk(25)
#> Class 'disk'
#> [1] 34 24 46 29 29 7 27 50 49 28 49 6 14 35 40 14 33 47 37 25 28 41 6 48 47
random_sir(25)
#> Class 'sir'
#> [1] R I R S S R I R I S I I S R R I I R S I S I R 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] 0.002 0.25 0.25 4 0.025 8 128 0.025 32 0.002
#> [11] 0.005 64 0.002 4 0.01 4 0.001 0.01 4 0.0625
#> [21] 0.005 4 2 1 128
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 4 4 2 >=16 >=16 2 4 8 8 >=16 8 2 2 4
#> [16] 2 4 2 >=16 2 2 >=16 <=1 2 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 2 1 0.25 4 1 0.25 <=0.125 <=0.125
#> [10] 0.25 4 4 <=0.125 4 0.25 1 <=0.125 1
#> [19] 2 2 0.25 0.25 4 <=0.125 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 44 39 37 49 11 40 17 49 10 37 15 20 22 47 41 29 39 15 35 49 11 37 40 41 44
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 15 15 12 14 17 16 15 11 14 16 15 14 14 12 12 12 15 13 16 12 15 12 14 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 15 15 22 27 15 20 17 22 22 15 18 21 17 21 25 20 24 17 17 27 19 19 26 16
# }