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 agent, the generated results will reflect reality as much as possible.
Usage
random_mic(size = NULL, mo = NULL, ab = NULL, ...)
random_disk(size = NULL, mo = NULL, ab = NULL, ...)
random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...)Arguments
- size
desired size of the returned vector. If used in a data.frame call or
dplyrverb, will get the current (group) size if left blank.- mo
any character that can be coerced to a valid microorganism code with
as.mo()- ab
any character that can be coerced to a valid antimicrobial agent code with
as.ab()- ...
ignored, only in place to allow future extensions
- prob_RSI
a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)
Details
The base R function sample() is used for generating values.
Generated values are based on the EUCAST 2022 guideline as implemented in the rsi_translation data set. To create specific generated values per bug or drug, set the mo and/or ab argument.
Examples
random_mic(25)
#> Class 'mic'
#> [1] 1 0.002 64 0.002 0.002 0.025 32 256 4 0.005
#> [11] 0.005 0.125 16 0.01 8 16 0.001 0.001 4 0.0625
#> [21] 16 0.01 0.25 1 1
random_disk(25)
#> Class 'disk'
#> [1] 46 14 7 43 47 45 46 44 10 23 43 50 26 36 9 41 8 11 30 7 30 40 44 29 46
random_rsi(25)
#> Class 'rsi'
#> [1] S R S I S S I I I I R R I R R I S I S I I I S R S
# \donttest{
# make the random generation more realistic by setting a bug and/or drug:
random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
#> Class 'mic'
#> [1] 0.002 32 <=0.001 0.0625 4 0.01 4 0.125 0.5
#> [10] 0.005 0.005 64 64 32 2 64 0.0625 1
#> [19] 1 0.025 0.002 0.125 16 32 0.002
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 16 8 16 1 1 16 <=0.25 4 8 <=0.25
#> [11] 1 0.5 16 4 8 0.5 <=0.25 8 2 8
#> [21] 0.5 2 4 0.5 8
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.0625 0.5 8 4 0.125 <=0.0625 4 8
#> [9] 0.5 4 8 0.125 0.125 4 <=0.0625 8
#> [17] <=0.0625 1 8 <=0.0625 8 2 8 0.125
#> [25] 8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 14 19 49 39 22 34 20 9 32 43 45 8 47 37 20 49 49 37 48 19 21 44 44 28 43
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 17 15 13 15 14 14 11 12 15 16 11 16 11 13 16 12 17 13 16 11 12 11 11 13 11
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 23 24 15 26 15 22 18 15 16 16 23 19 24 20 17 25 16 27 21 16 23 18 19 20
# }