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 8 4 0.01 0.25 <=0.001 2 0.5 0.125
#> [10] 4 0.005 1 32 64 0.01 >=128 0.25 0.0625
#> [19] 0.025 4 0.125 64 0.005 0.5 0.0625
random_disk(25)
#> Class 'disk'
#> [1] 41 41 50 42 9 18 6 13 38 13 35 13 26 24 22 49 42 10 49 49 35 24 42 41 41
random_sir(25)
#> Class 'sir'
#> [1] R S S R R R I S R S R R S S R R I I S R I I S 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] <=0.001 0.002 <=0.001 0.125 0.005 32 0.025 32 64
#> [10] 0.0625 8 0.125 64 0.025 1 1 0.025 0.002
#> [19] <=0.001 0.005 0.125 0.002 <=0.001 32 0.125
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] <=1 <=1 4 <=1 16 4 16 64 32 2 2 64 32 2 64 16 <=1 16 64
#> [20] 4 2 4 4 8 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 16 16 16 16 <=0.0625 8 8 4
#> [9] 8 <=0.0625 1 0.5 2 0.5 8 8
#> [17] 0.125 8 2 0.125 <=0.0625 0.125 0.25 2
#> [25] 0.25
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 40 32 46 40 24 29 50 24 47 40 31 11 48 41 38 9 48 42 39 14 9 48 39 29 24
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 16 16 17 13 15 11 15 17 17 11 12 16 12 13 14 11 14 13 16 12 11 13 12 11 13
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 16 21 23 18 19 27 19 27 16 23 15 16 27 17 15 26 21 27 20 24 26 24 24 19
# }