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# Random MIC Values/Disk Zones/SIR Generation

Source: `R/random.R`
`random.Rd`

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,
      skew = "right",
      severity = 1,
      ...
    )

    random_disk(
      size = NULL,
      mo = NULL,
      ab = NULL,
      skew = "left",
      severity = 1,
      ...
    )

    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()`. Can be the same length as `size`.

ab

  Any character that can be coerced to a valid antimicrobial drug code with `as.ab()`.

skew

  Direction of skew for MIC or disk values, either `"right"` or `"left"`. A left-skewed distribution has the majority of the data on the right.

severity

  Skew severity; higher values will increase the skewedness. Default is `2`; use `0` to prevent skewedness.

...

  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

Internally, MIC and disk zone values are sampled based on clinical breakpoints defined in the clinical_breakpoints data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument. The MICs are sampled on a log2 scale and disks linearly, using weighted probabilities. The weights are based on the `skew` and `severity` arguments:

- `skew = "right"` places more emphasis on lower MIC or higher disk values.

- `skew = "left"` places more emphasis on higher MIC or lower disk values.

- `severity` controls the exponential bias applied.

## Examples

    random_mic(25)
    #> Class <mic>
    #>  [1] 0.25   0.064  0.5    0.004  0.0001 0.032  0.008  16     0.016  0.125
    #> [11] 0.0002 0.001  0.008  0.004  0.064  256    0.5    32     512    0.0002
    #> [21] 0.004  1      0.002  0.0005 0.064
    random_disk(25)
    #> Class <disk>
    #>  [1] 49 44 31 11 27 33 39 24 19 43 30 44 33 31 22 13 37 19 26 29 44 12 46 18 27
    random_sir(25)
    #> Class <sir>
    #>  [1] I R I S R S R R I R R I S S S I R R S I R S R I R

    # add more skewedness, make more realistic by setting a bug and/or drug:
    disks <- random_disk(100, severity = 2, mo = "Escherichia coli", ab = "CIP")
    plot(disks)

    # `plot()` and `ggplot2::autoplot()` allow for coloured bars if `mo` and `ab` are set
    plot(disks, mo = "Escherichia coli", ab = "CIP", guideline = "CLSI 2025")

    # \donttest{
    random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
    #> Class <mic>
    #>  [1] 0.004  0.0002 0.008  0.25   0.0005 0.0002 8      0.032  0.0005 0.016
    #> [11] 0.032  32     1      0.0005 0.016  0.002  0.016  0.0005 0.004  0.25
    #> [21] 0.0005 0.016  0.001  0.25   0.032
    random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
    #> Class <mic>
    #>  [1] 0.5 >=1 0.5 0.5 0.5 0.5 >=1 0.5 0.5 0.5 0.5 0.5 0.5 0.5 >=1 0.5 >=1 0.5 0.5
    #> [20] 0.5 0.5 >=1 >=1 >=1 >=1
    random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
    #> Class <mic>
    #>  [1] 0.25    <=0.125 <=0.125 0.25    0.25    <=0.125 0.25    0.25    0.25
    #> [10] 0.25    <=0.125 <=0.125 0.25    0.25    <=0.125 <=0.125 <=0.125 0.25
    #> [19] <=0.125 <=0.125 <=0.125 <=0.125 0.25    0.25    0.25

    random_disk(25, "Klebsiella pneumoniae") # range 8-50
    #> Class <disk>
    #>  [1] 10 32 34 18 17 31 31 21 18 19 27 18 20 11 34 30 28 20 29  9 21 33 34 25 17
    random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
    #> Class <disk>
    #>  [1] 17 17 20 22 13 21 21 14 11 18 18 18 21 18 14 22 19 20 18 16 17 12 22 21 19
    random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
    #> Class <disk>
    #>  [1] 24 31 26 26 33 16 29 17 28 27 27 35 33 33 29 32 18 33 33 29 28 32 25 17 31
    # }