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] 0.125 0.001 1 16 0.025 0.002 0.125 2 128 0.01
#> [11] 256 64 256 0.005 2 32 0.0625 8 0.025 0.25
#> [21] 0.005 0.01 0.002 128 0.001
random_disk(25)
#> Error in seq.default(from = as.integer(min(df$breakpoint_R)/1.25), to = as.integer(max(df$breakpoint_S) * 1.25), by = 1): 'from' must be a finite number
random_rsi(25)
#> Class 'rsi'
#> [1] I I R S S S S R I S S I I I S S I I R R R R S I 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] 0.0625 32 2 >=128 0.25 0.25 0.125 64 4 4
#> [11] 0.01 0.5 1 >=128 0.25 8 8 64 32 0.25
#> [21] 0.002 0.01 0.005 0.005 0.005
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class 'mic'
#> [1] 4 >=32 4 0.5 4 4 <=0.25 <=0.25 >=32 >=32
#> [11] 1 16 >=32 >=32 1 1 0.5 >=32 16 4
#> [21] <=0.25 2 2 2 2
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class 'mic'
#> [1] 0.5 0.0625 4 4 0.125 <=0.025 0.125 2 4
#> [10] 0.0625 <=0.025 0.0625 2 2 8 0.0625 1 <=0.025
#> [19] <=0.025 0.25 4 <=0.025 <=0.025 0.25 0.5
random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class 'disk'
#> [1] 18 30 42 26 20 26 42 10 19 34 48 49 34 49 27 29 44 32 9 17 32 13 25 40 18
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class 'disk'
#> [1] 14 13 17 17 14 15 13 16 13 15 11 13 15 13 16 15 12 15 17 14 16 13 13 12 15
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class 'disk'
#> [1] 26 17 19 16 25 23 19 26 16 15 22 16 22 24 20 26 26 23 22 26 15 25 17 19 15
# }