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] 8 1 32 8 32 0.0625 8 2 <=0.001
#> [10] 0.125 <=0.001 64 64 16 4 <=0.001 64 256
#> [19] 0.25 1 0.002 0.25 256 0.0625 0.0625
random_disk(25)
#> Class 'disk'
#> [1] 40 47 29 40 17 8 22 45 49 26 35 9 50 48 31 18 47 43 41 45 47 29 10 49 49
random_sir(25)
#> Class 'sir'
#> [1] I R R S I I S R I R S S S S R I I R R S I I R 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] 16 0.005 64 2 0.5 0.25 2 0.001 0.01 256
#> [11] 128 1 16 0.5 0.0625 0.25 256 1 64 4
#> [21] 8 64 32 0.001 0.001
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 1 64 2 4 1 <=0.25 32 1 8 16
#> [11] 32 32 4 2 0.5 2 32 32 2 0.5
#> [21] 1 8 2 16 32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 0.25 >=16 <=0.0625 2 2 8 0.25
#> [9] 1 0.25 4 <=0.0625 2 2 4 >=16
#> [17] 0.5 2 4 0.125 0.25 4 0.125 0.25
#> [25] 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 43 43 40 48 24 23 43 21 33 10 16 45 18 30 50 39 23 48 44 16 41 15 50 43 35
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 16 15 13 17 16 16 14 13 11 16 11 15 11 15 15 11 13 12 15 17 12 11 13 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 23 27 15 19 19 18 18 22 22 21 23 27 18 27 23 25 15 26 22 20 24 16 26 19 17
# }