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 8 2 64 64 0.002 4 0.025 <=0.001
#> [10] 0.01 16 0.5 <=0.001 1 64 0.5 0.002 0.125
#> [19] 0.025 8 0.025 8 >=256 0.005 0.5
random_disk(25)
#> Class 'disk'
#> [1] 17 34 17 49 40 28 47 24 44 6 31 46 41 47 36 15 48 49 44 50 18 49 44 20 27
random_sir(25)
#> Class 'sir'
#> [1] S S S S S I S R R R I R I S R I I I S I S S I R S
# \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] 64 0.25 0.125 <=0.001 0.005 2 <=0.001 0.005 16
#> [10] 2 32 0.01 0.005 0.25 <=0.001 0.125 2 16
#> [19] 0.025 0.25 0.005 4 0.025 8 64
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 4 >=32 1 8 >=32 0.5 4 4 8 0.5 16 8 4 4
#> [16] 16 4 1 4 0.5 0.5 >=32 2 >=32 >=32
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 0.25 2 4 2 0.5 0.25 0.0625 0.125 >=8
#> [11] 4 4 0.125 2 0.5 2 0.125 >=8 1 2
#> [21] 4 0.5 0.125 0.25 >=8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 36 47 48 24 19 50 34 23 39 40 21 36 25 37 31 43 8 45 47 37 22 48 12 21 43
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 11 13 13 11 11 14 11 15 11 12 15 14 17 15 17 17 12 13 17 12 13 11 11 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 22 20 19 27 17 24 18 27 15 18 22 18 21 24 15 22 19 21 20 21 18 20 21 23
# }