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] <=0.002 2 0.5 >=128 0.005 0.25 0.01 8 2
#> [10] 2 32 0.005 0.025 0.25 0.125 16 8 0.01
#> [19] 0.005 0.025 0.005 0.5 <=0.002 16 0.0625
random_disk(25)
#> Class 'disk'
#> [1] 43 16 27 40 24 42 19 12 41 20 29 19 9 28 46 11 40 47 13 40 9 47 46 50 36
random_sir(25)
#> Class 'sir'
#> [1] I R S S S I R I R I R I R R I S S R S S I I I I S
# \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 0.001 8 64 0.025 0.0625 0.025 0.001 0.025 128
#> [11] 0.25 0.001 64 0.125 0.01 32 64 8 256 0.5
#> [21] 0.25 0.005 1 32 0.01
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 <=0.25 4 4 >=16 1 <=0.25 8 2 8
#> [11] 8 >=16 2 8 0.5 8 4 <=0.25 0.5 8
#> [21] 8 >=16 4 8 0.5
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 2 2 >=4 0.5 0.5 <=0.0625 1 >=4
#> [9] 0.5 2 0.5 >=4 0.125 0.25 1 0.125
#> [17] <=0.0625 2 1 0.125 0.5 0.5 0.25 0.25
#> [25] 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 45 41 33 18 10 50 49 47 31 35 22 29 14 39 47 38 24 40 45 43 9 24 50 10 30
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 13 14 17 13 16 17 14 15 17 16 14 17 14 12 17 12 14 14 16 13 17 13 15 13 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 15 15 25 19 21 26 19 22 26 21 26 17 25 21 19 19 20 22 15 19 16 24 19 15 19
# }