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] 0.25 8 64 2 32 2 0.01 4 0.005
#> [10] 0.25 0.0625 0.005 8 32 4 4 >=256 0.25
#> [19] 0.025 0.025 0.025 <=0.002 4 32 >=256
random_disk(25)
#> Class 'disk'
#> [1] 7 23 41 25 42 15 16 30 42 50 7 26 45 23 43 46 32 26 28 50 44 48 37 42 34
random_sir(25)
#> Class 'sir'
#> [1] R S I I I R S S S R I S S R R R I S R R S R I 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] 32 8 <=0.001 0.01 2 8 0.5 1 128
#> [10] 0.25 0.0625 0.025 4 0.01 0.125 0.25 0.25 0.125
#> [19] 32 32 0.01 1 0.01 0.25 32
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 64 16 32 64 32 2 2 1 64 8 4 0.5 8 32 8 64 4 32
#> [20] 64 4 4 16 2 1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 2 0.25 0.025 >=16 2 >=16 0.0625 0.125 8
#> [11] 0.125 1 0.0625 0.125 1 1 0.025 0.5 0.25 1
#> [21] 0.25 1 0.025 0.0625 0.0625
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 26 30 21 13 11 43 45 9 23 49 44 12 30 34 14 30 17 12 30 42 49 43 23 31 45
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 16 16 12 11 13 14 15 13 17 11 11 14 16 12 11 15 15 11 14 11 14 13 12 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 24 25 23 17 21 26 20 19 22 27 23 15 24 19 22 25 26 18 25 21 22 15 23 23 27
# }