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 64 0.25 0.002 128 128 2 1 1 4
#> [11] 32 4 4 2 0.025 64 8 32 0.25 0.5
#> [21] 0.002 16 32 0.0625 1
random_disk(25)
#> Class 'disk'
#> [1] 14 40 9 45 33 41 31 50 48 24 13 27 29 26 50 46 48 43 7 34 48 40 45 18 24
random_sir(25)
#> Class 'sir'
#> [1] R I S S S S S S I R R I S R S I R R I R R S S 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] 0.5 0.002 0.25 0.001 0.025 0.125 32 8 1 2
#> [11] 0.01 32 0.01 0.005 0.005 32 4 32 8 8
#> [21] 0.0625 4 0.5 0.001 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 8 16 <=1 2 2 4 4 4 8 <=1 <=1 <=1 <=1 8 2 16 4 8
#> [20] 32 16 8 2 16 <=1
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 0.125 1 1 0.125 0.25 0.25 >=4 2 2 2 0.25
#> [13] 0.25 0.125 1 0.25 >=4 0.125 >=4 0.5 >=4 0.25 0.25 0.125
#> [25] 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 47 32 35 46 12 40 42 20 46 25 31 40 31 40 40 42 29 49 26 19 42 13 43 23 47
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 15 12 12 11 15 16 17 12 12 16 15 16 15 11 13 12 17 14 14 17 12 15 12 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 19 25 20 18 15 20 19 21 22 15 15 18 20 25 16 25 24 23 26 21 25 21 25 22 16
# }