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] >=64 16 0.25 0.5 16 2 0.125 0.125 0.125
#> [10] 0.125 0.0625 16 <=0.001 <=0.001 >=64 32 0.01 4
#> [19] 1 >=64 0.005 4 1 0.01 32
random_disk(25)
#> Class 'disk'
#> [1] 38 25 43 6 40 45 43 47 21 21 35 44 19 41 11 20 25 39 16 47 35 49 40 12 6
random_sir(25)
#> Class 'sir'
#> [1] R I R I S R S I R I S R R S R R R I I S S R S I 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] 0.125 128 4 0.001 0.002 128 0.01 0.025 0.002 0.005 2 16
#> [13] 8 0.025 0.002 4 1 0.5 16 0.005 64 1 16 4
#> [25] 0.5
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 2 8 4 4 2 >=16 8 >=16 4 8 2 2 <=1 4 <=1
#> [16] <=1 <=1 8 4 >=16 >=16 2 <=1 8 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 4 0.25 4 0.025 0.5 2 >=8 4 0.5 1
#> [11] 0.25 0.025 >=8 0.5 0.5 0.025 0.125 0.0625 1 0.25
#> [21] 0.25 4 1 1 0.125
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 38 20 33 33 26 20 49 22 12 42 40 29 45 42 48 30 50 37 21 27 50 50 43 49 46
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 13 13 16 16 11 12 15 14 11 14 15 11 12 11 13 15 13 17 17 16 11 13 11 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 27 16 21 16 18 26 19 21 19 18 16 19 17 18 19 21 18 23 26 25 18 19 24 23 22
# }