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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 dplyr verb, 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)

Value

class mic for random_mic() (see as.mic()) and class disk for random_disk() (see as.disk())

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] 2      256    0.005  0.5    0.001  64     0.0625 0.005  0.005  0.001 
#> [11] 0.125  0.0625 0.0625 0.002  32     2      0.0625 4      2      0.125 
#> [21] 0.005  0.002  0.005  16     128   
random_disk(25)
#> Class 'disk'
#>  [1] 27 33 26 44 31 47 13 50 24  9 44  6 44 50  7 45  9 21 41 23 15  9 42  9 40
random_sir(25)
#> Class 'sir'
#>  [1] R R I R S R I R S I S R R S R I S R I S I I 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] 0.01    0.25    <=0.001 16      0.002   0.125   4       0.25    >=64   
#> [10] 1       <=0.001 0.005   0.125   0.025   <=0.001 2       0.5     <=0.001
#> [19] 0.002   0.25    0.0625  0.025   0.25    0.25    0.01   
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#>  [1] 32     16     0.5    8      4      <=0.25 2      1      2      0.5   
#> [11] 4      0.5    4      16     8      8      <=0.25 4      32     32    
#> [21] 0.5    0.5    16     0.5    16    
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#>  [1] 0.25   >=8    0.5    0.0625 0.5    0.0625 0.25   0.5    4      4     
#> [11] 4      1      1      >=8    >=8    >=8    2      0.25   0.25   2     
#> [21] >=8    >=8    0.5    0.25   1     

random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#>  [1] 17 47 43 49  8 36 33 21 38 30 39 13 41 22 47 21 19 12 47 12 36 46 48 47 27
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#>  [1] 15 11 17 17 11 17 12 17 16 17 16 13 13 12 16 14 13 11 11 12 13 11 13 12 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#>  [1] 20 17 19 16 20 24 17 23 19 25 27 19 22 19 23 18 23 24 21 24 26 21 27 18 17
# }