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 2023 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] 32 1 0.01 0.005 32 0.025 >=256 32 0.025 0.005 0.25 2
#> [13] 0.001 8 16 0.001 8 64 8 16 0.001 0.002 0.025 16
#> [25] 16
random_disk(25)
#> Class 'disk'
#> [1] 31 19 46 34 39 11 18 21 43 6 50 28 15 48 11 50 42 30 25 29 49 22 50 20 6
random_sir(25)
#> Class 'sir'
#> [1] I I R R S R I R I R I I S S R I S S I I S R S S S
# \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 0.001 0.01 128 0.002 16 0.01 0.002 0.025 256
#> [11] 8 0.025 0.002 2 256 0.25 0.125 16 2 0.002
#> [21] 16 128 128 128 0.0625
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 1 16 16 32 32 2 16 0.5 8 32 8 8 8 32 32 16 4 1
#> [20] 2 4 8 4 16 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 2 >=4 <=0.0625 0.5 1 0.25 2
#> [9] 1 >=4 1 0.125 2 0.25 1 >=4
#> [17] 1 2 2 >=4 >=4 1 0.25 >=4
#> [25] 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 48 11 40 10 50 25 40 49 42 18 32 47 27 36 36 13 42 50 47 18 49 14 50 39 12
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 15 15 11 17 13 17 11 16 13 12 13 15 13 16 12 12 16 13 15 17 16 11 14 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 16 16 21 17 24 20 15 24 23 17 16 25 16 19 15 18 27 26 21 27 27 19 27 26
# }