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] 0.025 0.025 0.125 8 0.25 0.0625 16 8 32
#> [10] 0.5 0.025 <=0.002 128 4 4 0.005 0.125 0.005
#> [19] 1 >=256 0.025 1 128 <=0.002 8
random_disk(25)
#> Class 'disk'
#> [1] 40 10 6 38 23 35 41 6 43 42 36 15 7 47 34 41 42 16 7 9 50 50 36 49 24
random_sir(25)
#> Class 'sir'
#> [1] S I R R I R R R R S S I R I R I I I R S S I S 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] <=0.001 2 0.25 0.005 0.01 4 1 >=256 0.025
#> [10] 128 0.01 0.025 <=0.001 128 <=0.001 >=256 32 64
#> [19] 0.25 0.005 >=256 64 64 32 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 16 1 4 8 32 32 >=64 >=64 32 16 1 4 32 32
#> [16] 4 32 4 4 >=64 1 16 16 16 >=64
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] >=4 2 0.5 >=4 1 0.25 1 1
#> [9] 0.25 <=0.0625 0.125 0.25 2 0.25 2 0.125
#> [17] 0.125 2 >=4 2 0.125 0.5 >=4 <=0.0625
#> [25] >=4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 21 44 48 15 21 12 34 43 45 20 41 12 45 29 12 47 48 37 27 9 26 49 38 16 16
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 13 17 17 13 15 17 16 11 15 16 16 15 11 16 14 16 17 12 13 17 12 13 16 14
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 21 23 25 18 21 20 16 20 21 15 26 25 18 24 17 26 24 24 21 15 18 15 15 16 15
# }