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 0.01 0.25 1 16 4 0.0625 0.005 0.5 0.005
#> [11] 0.025 256 128 32 0.01 4 0.005 0.001 2 0.0625
#> [21] 4 4 16 0.125 0.01
random_disk(25)
#> Class 'disk'
#> [1] 43 43 40 49 24 32 42 15 28 36 39 23 9 34 41 26 47 41 46 41 44 16 44 41 9
random_sir(25)
#> Class 'sir'
#> [1] R S S R S S S R S I S R S S R R R S R I I I S S R
# \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] 0.0625 64 0.002 0.125 0.01 0.25 16 0.125 0.0625 0.01
#> [11] 0.0625 0.01 0.025 0.5 1 2 0.01 0.0625 0.001 128
#> [21] 0.125 0.25 0.025 0.001 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 1 2 4 2 0.25 2 8 0.5 0.5 2 0.25 8 16 0.5 16
#> [16] 0.5 16 16 2 0.25 16 4 0.25 2 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 0.25 1 <=0.125 4 <=0.125 0.25 0.5 2
#> [10] 16 <=0.125 8 0.5 2 0.25 4 16 <=0.125
#> [19] 0.25 1 1 8 8 2 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 45 50 48 9 44 50 44 48 18 49 48 47 32 42 14 11 16 42 45 9 34 50 39 8 12
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 11 15 11 11 12 15 14 11 16 11 16 13 13 15 12 17 12 11 12 15 17 16 16 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 25 27 22 17 18 17 16 23 18 18 20 26 17 25 19 15 27 20 24 20 23 25 15 19
# }