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] 0.01 0.25 64 4 8 0.125 16 0.125 128
#> [10] 4 64 2 2 1 0.005 0.0625 2 0.125
#> [19] <=0.001 0.025 256 8 2 128 0.5
random_disk(25)
#> Class 'disk'
#> [1] 39 21 49 46 49 48 32 49 18 43 8 14 50 31 38 18 36 47 42 50 18 47 50 17 13
random_sir(25)
#> Class 'sir'
#> [1] I R S R R I R I R I I R I S R S R S S S I I I R 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 0.001 0.025 32 4 8 0.002 1 0.002 0.002 1 0.005
#> [13] 4 0.025 >=128 4 8 0.002 0.001 0.5 0.01 >=128 0.001 >=128
#> [25] 4
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=1 <=1 2 4 4 4 <=1 8 8 8 <=1 <=1 4 4 8
#> [16] 2 <=1 2 4 4 <=1 8 >=16 4 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.125 1 0.25 0.5 0.125 4 0.025 4 0.025 0.125
#> [11] 0.025 0.25 4 >=8 0.5 0.125 0.025 0.025 0.5 0.25
#> [21] 0.0625 0.125 2 0.0625 0.025
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 39 45 17 46 43 35 44 42 26 40 9 14 49 40 46 48 8 43 31 47 47 39 40 13 42
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 16 17 12 13 12 11 16 11 13 17 15 14 17 14 13 16 16 11 12 13 14 14 14 16
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 22 26 18 15 21 26 23 22 16 22 27 25 15 24 16 23 20 19 18 23 24 15 27 18 17
# }