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] 16 0.01 0.025 0.25 0.01 0.0625 0.001 16 0.01 128
#> [11] 16 64 0.01 0.5 0.005 4 64 0.002 0.125 0.01
#> [21] 0.0625 0.001 0.025 0.5 >=256
random_disk(25)
#> Class 'disk'
#> [1] 41 50 9 45 7 8 44 29 22 7 44 30 28 20 38 50 38 40 18 12 13 35 50 8 12
random_sir(25)
#> Class 'sir'
#> [1] S I S R S I S R S R S R I I S S I S S I I 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] 32 0.01 0.5 8 2 16 0.01 0.005 >=64 0.025
#> [11] 0.01 0.0625 >=64 2 0.025 16 8 0.001 0.01 >=64
#> [21] 1 32 2 >=64 0.25
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 8 32 >=64 8 <=1 2 2 <=1 8 8 16 2 32 4 2
#> [16] <=1 8 <=1 <=1 32 4 4 >=64 32 16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.25 0.25 0.5 0.25 0.125 4 8 8
#> [9] 1 0.125 1 <=0.0625 4 <=0.0625 <=0.0625 1
#> [17] 0.125 1 0.125 2 2 4 4 1
#> [25] 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 12 46 47 45 33 42 43 46 46 50 41 41 50 21 50 33 17 18 43 25 47 8 25 22 50
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 11 15 16 16 16 15 16 16 11 15 15 11 12 16 16 13 15 14 17 14 17 12 15 13 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 16 25 17 26 18 23 20 17 15 24 20 23 20 16 24 27 25 17 23 25 25 25 24 25 17
# }