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138 lines
4.5 KiB
Markdown
138 lines
4.5 KiB
Markdown
# Random MIC Values/Disk Zones/SIR Generation
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These functions can be used for generating random MIC values and disk
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diffusion diameters, for AMR data analysis practice. By providing a
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microorganism and antimicrobial drug, the generated results will reflect
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reality as much as possible.
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## Usage
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``` r
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random_mic(size = NULL, mo = NULL, ab = NULL, skew = "right",
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severity = 1, ...)
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random_disk(size = NULL, mo = NULL, ab = NULL, skew = "left",
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severity = 1, ...)
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random_sir(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...)
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```
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## Arguments
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- size:
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Desired size of the returned vector. If used in a
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[data.frame](https://rdrr.io/r/base/data.frame.html) call or `dplyr`
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verb, will get the current (group) size if left blank.
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- mo:
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Any [character](https://rdrr.io/r/base/character.html) that can be
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coerced to a valid microorganism code with
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[`as.mo()`](https://amr-for-r.org/reference/as.mo.md). Can be the same
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length as `size`.
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- ab:
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Any [character](https://rdrr.io/r/base/character.html) that can be
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coerced to a valid antimicrobial drug code with
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[`as.ab()`](https://amr-for-r.org/reference/as.ab.md).
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- skew:
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Direction of skew for MIC or disk values, either `"right"` or
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`"left"`. A left-skewed distribution has the majority of the data on
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the right.
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- severity:
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Skew severity; higher values will increase the skewedness. Default is
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`2`; use `0` to prevent skewedness.
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- ...:
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Ignored, only in place to allow future extensions.
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- prob_SIR:
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A vector of length 3: the probabilities for "S" (1st value), "I" (2nd
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value) and "R" (3rd value).
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## Value
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class `mic` for `random_mic()` (see
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[`as.mic()`](https://amr-for-r.org/reference/as.mic.md)) and class
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`disk` for `random_disk()` (see
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[`as.disk()`](https://amr-for-r.org/reference/as.disk.md))
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## Details
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Internally, MIC and disk zone values are sampled based on clinical
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breakpoints defined in the
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[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
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data set. To create specific generated values per bug or drug, set the
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`mo` and/or `ab` argument. The MICs are sampled on a log2 scale and
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disks linearly, using weighted probabilities. The weights are based on
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the `skew` and `severity` arguments:
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- `skew = "right"` places more emphasis on lower MIC or higher disk
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values.
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- `skew = "left"` places more emphasis on higher MIC or lower disk
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values.
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- `severity` controls the exponential bias applied.
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## Examples
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``` r
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random_mic(25)
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#> Class 'mic'
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#> [1] 0.008 0.125 4 32 1 0.004 0.008 0.0002
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#> [9] 0.125 2 0.008 0.008 0.016 0.125 0.064 <=0.0001
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#> [17] 0.0005 0.0002 0.5 0.002 0.002 0.25 16 <=0.0001
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#> [25] 0.002
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random_disk(25)
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#> Class 'disk'
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#> [1] 25 47 24 47 38 28 36 33 31 50 41 29 40 31 44 45 37 40 44 49 9 48 20 37 47
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random_sir(25)
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#> Class 'sir'
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#> [1] S S R R S S I S I S S I S R I I I I S I R I I I I
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# add more skewedness, make more realistic by setting a bug and/or drug:
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disks <- random_disk(100, severity = 2, mo = "Escherichia coli", ab = "CIP")
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plot(disks)
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# `plot()` and `ggplot2::autoplot()` allow for coloured bars if `mo` and `ab` are set
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plot(disks, mo = "Escherichia coli", ab = "CIP", guideline = "CLSI 2025")
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# \donttest{
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random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
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#> Class 'mic'
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#> [1] 2 0.001 4 0.008 0.0005 0.0005 0.0005 0.0002 0.0002 >=64
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#> [11] 0.0002 1 0.5 0.002 0.5 0.002 0.001 0.032 0.008 0.004
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#> [21] 0.032 0.0002 0.0005 0.002 0.001
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random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
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#> Class 'mic'
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#> [1] <=0.5 <=0.5 2 <=0.5 1 <=0.5 <=0.5 <=0.5 <=0.5 1 <=0.5 <=0.5
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#> [13] <=0.5 1 <=0.5 1 <=0.5 <=0.5 <=0.5 <=0.5 <=0.5 <=0.5 2 1
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#> [25] 2
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random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
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#> Class 'mic'
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#> [1] 0.125 0.125 1 0.25 0.5 0.125 0.125 0.125 0.125 0.125 0.125 0.125
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#> [13] 1 0.125 0.5 1 0.125 0.25 0.5 0.25 0.5 0.5 0.5 0.125
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#> [25] 0.25
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random_disk(25, "Klebsiella pneumoniae") # range 8-50
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#> Class 'disk'
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#> [1] 32 21 23 21 14 22 25 29 29 28 34 34 34 33 13 28 33 34 32 25 18 26 13 21 33
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random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
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#> Class 'disk'
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#> [1] 20 21 15 22 16 22 16 14 21 17 15 19 20 17 18 21 16 20 11 22 19 18 19 11 21
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random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
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#> Class 'disk'
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#> [1] 29 25 31 17 29 21 31 34 33 31 29 30 23 20 33 20 34 32 35 26 26 26 34 30 33
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# }
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```
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