mirror of
https://github.com/msberends/AMR.git
synced 2026-06-24 06:16:24 +02:00
150 lines
4.6 KiB
Markdown
150 lines
4.6 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] 1 0.032 0.064 1 0.25 0.125 >=128 0.0002 32 0.25
|
|
#> [11] 0.008 0.125 0.001 0.032 8 >=128 0.032 0.008 8 >=128
|
|
#> [21] 0.125 0.0001 0.5 64 1
|
|
random_disk(25)
|
|
#> Class <disk>
|
|
#> [1] 49 39 29 30 16 23 44 50 25 28 29 14 44 34 8 33 33 34 38 42 10 42 43 11 46
|
|
random_sir(25)
|
|
#> Class <sir>
|
|
#> [1] I S S S R R S R I I I I S R S I S S S R R I R S 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] 256 <=0.0001 <=0.0001 0.016 1 0.016 2 8
|
|
#> [9] 0.5 0.004 0.032 0.004 0.001 0.001 0.064 0.002
|
|
#> [17] 0.032 0.004 0.008 16 0.125 <=0.0001 0.001 0.008
|
|
#> [25] 0.001
|
|
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
|
|
#> Class <mic>
|
|
#> [1] 0.5 <=0.25 0.5 4 1 1 0.5 0.5 0.5 <=0.25
|
|
#> [11] 0.5 0.5 2 1 <=0.25 <=0.25 8 <=0.25 1 1
|
|
#> [21] <=0.25 0.5 16 2 0.5
|
|
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
|
|
#> Class <mic>
|
|
#> [1] 0.125 0.125 0.125 0.125 0.125 >=0.25 0.125 0.125 0.125 0.125
|
|
#> [11] >=0.25 0.125 >=0.25 0.125 0.125 0.125 >=0.25 0.125 >=0.25 >=0.25
|
|
#> [21] >=0.25 0.125 0.125 0.125 >=0.25
|
|
|
|
random_disk(25, "Klebsiella pneumoniae") # range 8-50
|
|
#> Class <disk>
|
|
#> [1] 18 32 21 19 23 10 30 18 22 34 19 32 28 18 25 7 27 23 28 17 29 18 22 28 23
|
|
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
|
|
#> Class <disk>
|
|
#> [1] 22 18 13 22 17 12 20 20 16 20 22 22 18 20 20 22 22 16 13 17 15 17 16 22 15
|
|
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
|
|
#> Class <disk>
|
|
#> [1] 31 30 30 28 24 35 28 34 28 29 27 29 24 21 13 16 34 19 26 20 27 32 32 24 26
|
|
# }
|
|
```
|