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reference/random.md

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+# 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] 0.008    0.016    0.25     0.5      0.5      1        0.002    0.002   
+#>  [9] 0.001    0.064    0.002    0.064    <=0.0002 1        4        0.016   
+#> [17] 0.008    8        0.25     0.5      0.5      0.032    4        0.008   
+#> [25] 0.004   
+random_disk(25)
+#> Class 'disk'
+#>  [1] 39 47 20 36 18 44 43 25 28 26 44 36 42  8 28 44 31 29 49 30 28 39 49 25 49
+random_sir(25)
+#> Class 'sir'
+#>  [1] I R S R S R R S I I I S R R S I I S I I I S S 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] 1      8      0.004  4      0.032  8      0.016  8      0.001  0.0002
+#> [11] 0.002  0.004  0.001  0.0005 0.0001 0.002  0.125  >=64   0.002  0.0005
+#> [21] 0.001  0.0002 0.0005 0.001  0.0005
+random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
+#> Class 'mic'
+#>  [1] <=0.5 <=0.5 <=0.5 1     <=0.5 <=0.5 <=0.5 <=0.5 <=0.5 <=0.5 1     1    
+#> [13] <=0.5 <=0.5 <=0.5 <=0.5 1     <=0.5 <=0.5 <=0.5 <=0.5 1     1     <=0.5
+#> [25] <=0.5
+random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
+#> Class 'mic'
+#>  [1] >=2 1   1   1   >=2 >=2 >=2 1   >=2 1   1   >=2 1   1   1   >=2 1   1   1  
+#> [20] >=2 >=2 1   1   1   1  
+
+random_disk(25, "Klebsiella pneumoniae") # range 8-50
+#> Class 'disk'
+#>  [1] 28 12 30 26  9 34 30 19 32 31 33 34 30 19 15 24 18 34 12 32 29 33 29 32 17
+random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
+#> Class 'disk'
+#>  [1] 18 15 19 13 22 20 22 13 18 14 19 13 12 22 20 21 12 20 18 19 20 22 18 17 20
+random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
+#> Class 'disk'
+#>  [1] 21 31 27 28 30 34 16 32 28 25 25 23 29 26 24 28 27 33 30 19 30 22 27 22 32
+# }
+```