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] <=0.001 >=256 0.0625 0.25 1 0.025 0.002 0.005 1
#> [10] 0.025 16 8 4 0.5 0.005 0.125 32 0.025
#> [19] 0.5 <=0.001 <=0.001 1 0.0625 >=256 0.01
random_disk(25)
#> Class 'disk'
#> [1] 10 17 19 43 50 18 50 14 49 16 47 28 27 48 40 21 49 44 50 23 12 10 46 19 48
random_sir(25)
#> Class 'sir'
#> [1] S R I R I R I I S R I I I R I R I I I I I R 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] 0.0625 0.001 0.001 64 0.025 0.25 1 0.0625 256 0.25
#> [11] 0.01 0.001 2 8 0.01 32 0.002 0.5 0.125 0.005
#> [21] 4 32 0.25 0.5 0.005
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 1 8 2 1 >=32 2 0.5 >=32 >=32 1 >=32 4 >=32 16
#> [16] 1 0.5 0.5 4 0.5 8 1 1 >=32 4
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.125 0.125 0.125 0.25 0.125 0.25 2 0.25 0.25 2 0.5 4
#> [13] 4 2 0.125 0.25 0.125 0.125 4 2 0.5 0.25 0.125 0.125
#> [25] 4
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 43 25 43 32 45 42 10 14 23 47 22 15 32 9 20 39 40 24 17 10 9 24 32 15 37
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 12 15 12 17 16 15 15 16 14 14 17 16 13 14 11 15 15 13 14 16 15 12 11 13 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 25 23 19 22 15 24 22 24 15 21 25 25 16 21 19 23 20 26 24 26 19 27 25 20 16
# }