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] 2 256 0.005 0.5 0.001 64 0.0625 0.005 0.005 0.001
#> [11] 0.125 0.0625 0.0625 0.002 32 2 0.0625 4 2 0.125
#> [21] 0.005 0.002 0.005 16 128
random_disk(25)
#> Class 'disk'
#> [1] 27 33 26 44 31 47 13 50 24 9 44 6 44 50 7 45 9 21 41 23 15 9 42 9 40
random_sir(25)
#> Class 'sir'
#> [1] R R I R S R I R S I S R R S R I S R I S I I I S 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] 0.01 0.25 <=0.001 16 0.002 0.125 4 0.25 >=64
#> [10] 1 <=0.001 0.005 0.125 0.025 <=0.001 2 0.5 <=0.001
#> [19] 0.002 0.25 0.0625 0.025 0.25 0.25 0.01
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 32 16 0.5 8 4 <=0.25 2 1 2 0.5
#> [11] 4 0.5 4 16 8 8 <=0.25 4 32 32
#> [21] 0.5 0.5 16 0.5 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 >=8 0.5 0.0625 0.5 0.0625 0.25 0.5 4 4
#> [11] 4 1 1 >=8 >=8 >=8 2 0.25 0.25 2
#> [21] >=8 >=8 0.5 0.25 1
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 17 47 43 49 8 36 33 21 38 30 39 13 41 22 47 21 19 12 47 12 36 46 48 47 27
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 11 17 17 11 17 12 17 16 17 16 13 13 12 16 14 13 11 11 12 13 11 13 12 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 20 17 19 16 20 24 17 23 19 25 27 19 22 19 23 18 23 24 21 24 26 21 27 18 17
# }