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] 16     0.01   0.025  0.25   0.01   0.0625 0.001  16     0.01   128
#> [11] 16     64     0.01   0.5    0.005  4      64     0.002  0.125  0.01
#> [21] 0.0625 0.001  0.025  0.5    >=256
random_disk(25)
#> Class 'disk'
#>  [1] 41 50  9 45  7  8 44 29 22  7 44 30 28 20 38 50 38 40 18 12 13 35 50  8 12
random_sir(25)
#> Class 'sir'
#>  [1] S I S R S I S R S R S R I I S S I S S I I S S S 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] 32     0.01   0.5    8      2      16     0.01   0.005  >=64   0.025
#> [11] 0.01   0.0625 >=64   2      0.025  16     8      0.001  0.01   >=64
#> [21] 1      32     2      >=64   0.25
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#>  [1] 8    32   >=64 8    <=1  2    2    <=1  8    8    16   2    32   4    2
#> [16] <=1  8    <=1  <=1  32   4    4    >=64 32   16
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#>  [1] 0.25     0.25     0.5      0.25     0.125    4        8        8
#>  [9] 1        0.125    1        <=0.0625 4        <=0.0625 <=0.0625 1
#> [17] 0.125    1        0.125    2        2        4        4        1
#> [25] 8

random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#>  [1] 12 46 47 45 33 42 43 46 46 50 41 41 50 21 50 33 17 18 43 25 47  8 25 22 50
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#>  [1] 11 15 16 16 16 15 16 16 11 15 15 11 12 16 16 13 15 14 17 14 17 12 15 13 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#>  [1] 16 25 17 26 18 23 20 17 15 24 20 23 20 16 24 27 25 17 23 25 25 25 24 25 17
# }