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] 4 4 128 4 4 2 0.25 0.002 2 128 1 0.25
#> [13] 128 0.5 0.005 0.025 4 256 64 16 16 0.01 0.25 0.001
#> [25] 0.002
random_disk(25)
#> Class 'disk'
#> [1] 42 9 27 42 18 9 46 39 38 20 26 48 6 47 40 23 13 29 22 6 8 16 40 20 16
random_sir(25)
#> Class 'sir'
#> [1] S S I I S S S I R R I R I I S R R R R I I S R I 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] 32 0.125 0.025 0.001 0.01 64 0.125 0.01 2 2 64 1
#> [13] 0.025 0.25 0.125 16 8 0.125 0.002 4 0.025 128 256 0.002
#> [25] 16
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 32 1 16 2 4 32 32 32 2 4 2 16 1 16 16 2 16 2 8 8 1 8 32 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.0625 0.25 4 0.5 0.5 2 16 1
#> [9] 0.5 <=0.0625 <=0.0625 0.25 0.125 8 1 0.125
#> [17] 0.25 0.25 0.5 4 <=0.0625 0.5 2 0.5
#> [25] <=0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 15 40 46 17 10 19 38 43 35 33 44 9 22 30 24 49 11 48 8 18 8 12 21 24 33
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 13 15 12 15 17 11 14 17 15 15 13 13 13 13 13 11 17 16 13 12 13 13 12 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 23 23 18 25 24 16 19 20 22 15 22 23 24 21 24 23 17 22 17 23 27 23 26 19
# }