# Random MIC Values/Disk Zones/SIR Generation

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

``` r
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](https://rdrr.io/r/base/data.frame.html) call or `dplyr`
  verb, will get the current (group) size if left blank.

- mo:

  Any [character](https://rdrr.io/r/base/character.html) that can be
  coerced to a valid microorganism code with
  [`as.mo()`](https://amr-for-r.org/reference/as.mo.md). Can be the same
  length as `size`.

- ab:

  Any [character](https://rdrr.io/r/base/character.html) that can be
  coerced to a valid antimicrobial drug code with
  [`as.ab()`](https://amr-for-r.org/reference/as.ab.md).

- 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()`](https://amr-for-r.org/reference/as.mic.md)) and class
`disk` for `random_disk()` (see
[`as.disk()`](https://amr-for-r.org/reference/as.disk.md))

## Details

Internally, MIC and disk zone values are sampled based on clinical
breakpoints defined in the
[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
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

``` r
random_mic(25)
#> Class 'mic'
#>  [1] 0.125    <=0.0001 0.004    0.004    0.5      0.032    1        0.008   
#>  [9] 128      0.0002   0.002    0.002    32       0.032    0.0005   0.0002  
#> [17] 0.008    0.001    0.0002   <=0.0001 0.064    0.016    0.008    4       
#> [25] 1       
random_disk(25)
#> Class 'disk'
#>  [1] 50 21 48 47 46 38 45 47 24 28 45 43 19 23 44 19 31 22 40 39 39 36 35 14 34
random_sir(25)
#> Class 'sir'
#>  [1] I S S R I S R I R I S S S R R R I I R R I S R R S

# 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] 0.0001 0.0002 0.016  0.5    0.008  >=8    0.125  0.0002 0.002  0.0005
#> [11] 1      0.0001 0.25   0.0002 0.25   2      0.0005 0.064  0.5    0.004 
#> [21] 0.001  0.064  0.032  0.0005 0.125 
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#>  [1] <=2 <=2 4   <=2 <=2 4   <=2 4   <=2 4   <=2 <=2 <=2 <=2 <=2 <=2 4   4   <=2
#> [20] 4   <=2 <=2 <=2 <=2 <=2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#>  [1] 2       <=0.064 1       <=0.064 <=0.064 2       <=0.064 0.25    0.25   
#> [10] 2       <=0.064 <=0.064 <=0.064 <=0.064 0.25    0.5     0.5     0.25   
#> [19] 0.125   0.125   4       0.25    1       <=0.064 <=0.064

random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#>  [1] 14 19 19 33 33 26 16 27 29 33 24 17 17 15 16 26 26 14 17 29 25 25 24 32 32
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#>  [1] 22 15 21 11 19 20 11 14 12 12 17 16 12 10 15 22 19 21 19 17 18 19 21 17 21
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#>  [1] 21 25 16 29 27 24 31 22 35 28 26 32 24 18 35 33 24 28 33 25 35 25 32 24 26
# }
```