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 64 8 64 128 4 0.25 8 0.002 4
#> [11] 0.01 128 0.0625 32 128 0.025 0.025 0.005 0.025 128
#> [21] 32 1 64 64 16
random_disk(25)
#> Class 'disk'
#> [1] 41 29 23 6 49 23 25 45 18 36 10 40 40 26 9 23 48 39 36 27 12 48 30 29 12
random_sir(25)
#> Class 'sir'
#> [1] I I I R I R R R I R S I R R I S I I I S R S I 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] 16 32 0.125 1 >=64 2 0.001 0.002 >=64 0.5 0.005 0.5
#> [13] 0.125 4 4 4 16 32 16 0.5 0.001 0.002 8 0.002
#> [25] 1
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 0.25 32 1 32 2 2 4 0.5 4 4 0.25 32 0.5 0.5 8
#> [16] 32 0.5 1 32 1 8 8 16 0.25 0.25
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.125 <=0.025 2 0.25 8 8 >=16 2 0.125
#> [10] 1 0.125 2 0.5 8 0.5 <=0.025 0.125 >=16
#> [19] 0.125 2 8 1 8 0.0625 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 35 44 14 44 42 36 19 46 26 44 40 40 18 12 22 48 20 8 25 42 37 21 21 50 50
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 11 12 12 11 14 12 17 17 11 16 13 12 11 11 16 16 11 11 16 16 15 17 12 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 24 16 21 17 15 20 23 15 20 24 16 21 21 18 19 26 17 22 22 19 17 24 18 17
# }