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] 64 0.125 4 0.25 64 128 0.125 128 256 0.001
#> [11] 0.5 1 0.5 0.25 0.001 256 128 0.0625 0.0625 0.01
#> [21] 0.001 0.125 0.002 0.005 0.001
random_disk(25)
#> Class 'disk'
#> [1] 43 40 47 19 6 8 26 46 43 13 48 14 24 43 45 29 42 46 6 19 19 47 28 17 41
random_rsi(25)
#> Class 'rsi'
#> [1] I I S S R R R I I R I R S S R R S S I R R S I R I
# \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] 8 4 0.002 0.01 0.005 0.0625 0.005 8 >=64 0.5
#> [11] 0.0625 >=64 0.001 0.01 0.25 0.0625 0.125 0.125 1 32
#> [21] 0.002 0.025 0.002 8 0.025
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 64 64 16 8 2 32 16 2 64 4 8 64 8 64 64 8 4 4 4
#> [20] 4 64 0.5 16 0.5 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] <=0.0625 0.125 1 <=0.0625 <=0.0625 <=0.0625 2 0.125
#> [9] <=0.0625 4 <=0.0625 0.25 >=8 1 0.125 4
#> [17] 2 0.125 <=0.0625 4 0.25 0.5 2 2
#> [25] >=8
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 19 40 40 47 26 36 39 28 33 48 12 45 31 40 42 39 45 37 42 12 45 46 32 10 24
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 15 14 17 11 16 14 12 12 16 13 11 15 15 12 13 17 17 13 15 16 11 15 16 12 12
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 18 17 18 16 21 21 23 17 17 26 15 19 18 23 23 18 22 24 21 25 26 15 26 19 24
# }