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 0.025 0.25 >=128 0.005 0.125 0.01 32 0.01 8 0.002 32
#> [13] 4 4 0.01 4 0.01 16 0.025 0.5 0.002 0.25 0.001 64
#> [25] 4
random_disk(25)
#> Class 'disk'
#> [1] 45 43 50 33 10 21 20 26 34 15 43 40 36 46 30 50 46 31 50 44 28 42 19 10 45
random_sir(25)
#> Class 'sir'
#> [1] R S R I I S S R I R S R I R S S S S R S S I S R 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] 0.25 16 0.5 64 0.25 >=128 4 1 >=128
#> [10] 1 32 0.005 0.002 2 0.5 64 32 0.0625
#> [19] <=0.001 >=128 0.002 0.005 4 64 0.25
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 32 1 0.5 1 1 1 4 32 0.5 8 64 1 64 64 4 1 4 2
#> [20] 2 2 4 32 1 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 0.125 0.25 0.125 0.5 0.5 0.25 1
#> [9] 2 0.25 0.5 <=0.0625 0.25 0.125 <=0.0625 0.125
#> [17] 0.125 0.125 4 0.25 0.5 0.125 1 0.5
#> [25] 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 38 38 25 42 21 30 49 29 14 31 23 20 45 21 19 50 32 16 41 43 23 9 27 22 28
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 16 17 11 12 17 17 15 15 16 17 15 14 16 15 16 17 13 15 14 13 12 13 15 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 17 25 24 20 19 17 16 23 24 23 23 25 26 25 26 19 17 23 17 25 19 19 23 20 25
# }