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148 lines
4.4 KiB
Markdown
148 lines
4.4 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(
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size = NULL,
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mo = NULL,
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ab = NULL,
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skew = "right",
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severity = 1,
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...
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)
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random_disk(
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size = NULL,
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mo = NULL,
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ab = NULL,
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skew = "left",
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severity = 1,
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...
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)
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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] 0.25 0.064 0.5 0.004 0.0001 0.032 0.008 16 0.016 0.125
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#> [11] 0.0002 0.001 0.008 0.004 0.064 256 0.5 32 512 0.0002
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#> [21] 0.004 1 0.002 0.0005 0.064
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random_disk(25)
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#> Class <disk>
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#> [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
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random_sir(25)
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#> Class <sir>
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#> [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
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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] 0.004 0.0002 0.008 0.25 0.0005 0.0002 8 0.032 0.0005 0.016
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#> [11] 0.032 32 1 0.0005 0.016 0.002 0.016 0.0005 0.004 0.25
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#> [21] 0.0005 0.016 0.001 0.25 0.032
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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 >=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
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#> [20] 0.5 0.5 >=1 >=1 >=1 >=1
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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] 0.25 <=0.125 <=0.125 0.25 0.25 <=0.125 0.25 0.25 0.25
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#> [10] 0.25 <=0.125 <=0.125 0.25 0.25 <=0.125 <=0.125 <=0.125 0.25
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#> [19] <=0.125 <=0.125 <=0.125 <=0.125 0.25 0.25 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] 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
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random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
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#> Class <disk>
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#> [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
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random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
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#> Class <disk>
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#> [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
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# }
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```
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