mirror of
https://github.com/msberends/AMR.git
synced 2026-03-16 00:47:49 +01:00
138 lines
4.5 KiB
Markdown
138 lines
4.5 KiB
Markdown
# 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 0.125 4 32 1 0.004 0.008 0.0002
|
|
#> [9] 0.125 2 0.008 0.008 0.016 0.125 0.064 <=0.0001
|
|
#> [17] 0.0005 0.0002 0.5 0.002 0.002 0.25 16 <=0.0001
|
|
#> [25] 0.002
|
|
random_disk(25)
|
|
#> Class 'disk'
|
|
#> [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
|
|
random_sir(25)
|
|
#> Class 'sir'
|
|
#> [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
|
|
|
|
# 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] 2 0.001 4 0.008 0.0005 0.0005 0.0005 0.0002 0.0002 >=64
|
|
#> [11] 0.0002 1 0.5 0.002 0.5 0.002 0.001 0.032 0.008 0.004
|
|
#> [21] 0.032 0.0002 0.0005 0.002 0.001
|
|
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
|
|
#> Class 'mic'
|
|
#> [1] <=0.5 <=0.5 2 <=0.5 1 <=0.5 <=0.5 <=0.5 <=0.5 1 <=0.5 <=0.5
|
|
#> [13] <=0.5 1 <=0.5 1 <=0.5 <=0.5 <=0.5 <=0.5 <=0.5 <=0.5 2 1
|
|
#> [25] 2
|
|
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
|
|
#> Class 'mic'
|
|
#> [1] 0.125 0.125 1 0.25 0.5 0.125 0.125 0.125 0.125 0.125 0.125 0.125
|
|
#> [13] 1 0.125 0.5 1 0.125 0.25 0.5 0.25 0.5 0.5 0.5 0.125
|
|
#> [25] 0.25
|
|
|
|
random_disk(25, "Klebsiella pneumoniae") # range 8-50
|
|
#> Class 'disk'
|
|
#> [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
|
|
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
|
|
#> Class 'disk'
|
|
#> [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
|
|
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
|
|
#> Class 'disk'
|
|
#> [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
|
|
# }
|
|
```
|