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] 128 0.25 0.01 1 0.005 32 0.0625 32 4
#> [10] 64 8 128 0.5 128 0.005 64 <=0.002 0.025
#> [19] 4 128 0.025 16 0.25 <=0.002 0.01
random_disk(25)
#> Class 'disk'
#> [1] 24 46 46 45 35 44 43 19 37 6 47 49 42 14 42 28 35 12 28 23 9 47 50 18 32
random_sir(25)
#> Class 'sir'
#> [1] I S I I I S S R I R I S R I I I R R I I R 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] 128 0.5 <=0.001 32 1 0.125 0.0625 0.25 4
#> [10] 64 0.125 0.025 64 0.002 1 8 2 128
#> [19] 32 1 2 0.005 0.01 1 0.005
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 32 <=1 8 2 8 16 32 4 2 4 2 <=1 2 8 <=1 16 <=1 8
#> [20] 32 <=1 32 8 8 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 4 4 4 0.0625 0.125 0.5 4 0.125 0.0625
#> [11] 0.25 0.0625 0.0625 16 8 0.25 0.25 2 0.125 0.0625
#> [21] 0.5 0.25 4 0.25 2
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 12 22 49 15 47 47 30 29 25 40 40 42 49 19 28 49 29 18 13 43 26 48 34 34 31
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 17 12 17 14 11 16 14 13 14 17 14 15 14 12 13 11 11 17 11 16 12 11 16 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 15 17 17 17 25 20 23 16 24 27 15 23 25 23 15 16 19 23 18 22 25 26 15 17
# }