Generate Random MIC Values, Disk Zones, or SIR Results

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

random_mic(
  size = NULL,
  mo = NULL,
  ab = NULL,
  skew = "right",
  severity = 1,
  guideline = getOption("AMR_guideline", "EUCAST"),
  ...
)

random_disk(
  size = NULL,
  mo = NULL,
  ab = NULL,
  skew = "left",
  severity = 1,
  guideline = getOption("AMR_guideline", "EUCAST"),
  ...
)

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 call or dplyr verb, will get the current (group) size if left blank.
mo: Any character that can be coerced to a valid microorganism code with as.mo(). Can be the same length as size.
ab: Any character that can be coerced to a valid antimicrobial drug code with as.ab().
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.
guideline: A guideline name to base the generated values on, either "EUCAST" (default) or "CLSI" for the latest implemented version, or a guideline including a year (e.g., "CLSI 2019"). The default can be changed with the package option AMR_guideline, see as.sir().
...: 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()) and class disk for random_disk() (see as.disk())

Details

Internally, MIC and disk zone values are sampled based on the human clinical breakpoints of guideline in the clinical_breakpoints 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

random_mic(25)
#> Class <mic>
#>  [1] 0.002  0.0005 0.125  0.0005 0.5    0.008  0.008  2      >=8    0.016 
#> [11] 0.008  0.25   0.016  0.008  0.002  0.0002 0.0002 0.0002 0.125  0.001 
#> [21] 1      0.125  0.5    0.002  0.016 
random_disk(25)
#> Class <disk>
#>  [1] 46 48 39 28 25 42 40 50 46 34 29 20 35 29 20 41 38 18 24 28 49 24 46 41 23
random_sir(25)
#> Class <sir>
#>  [1] I R I S R I I R I S S I I R S I R I I S I I I R S

# 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")


# \donttest{
random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
#> Class <mic>
#>  [1] 4      0.001  0.004  0.0001 0.002  0.008  0.008  1      0.125  0.064 
#> [11] >=16   0.002  0.0001 0.0002 0.0001 0.064  0.0002 0.001  0.002  0.0005
#> [21] 0.0005 0.016  0.004  0.0005 0.0005
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
#> Class <mic>
#>  [1] <=2 <=2 <=2 <=2 4   <=2 4   <=2 4   <=2 4   4   4   <=2 4   <=2 <=2 4   <=2
#> [20] 4   4   <=2 <=2 <=2 4  
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
#> Class <mic>
#>  [1] <=0.064 <=0.064 <=0.064 0.25    <=0.064 0.25    <=0.064 <=0.064 0.25   
#> [10] <=0.064 <=0.064 0.125   0.125   <=0.064 0.125   0.25    0.125   <=0.064
#> [19] 0.125   <=0.064 0.125   0.25    0.25    <=0.064 <=0.064

random_disk(25, "Klebsiella pneumoniae") # range 8-50
#> Class <disk>
#>  [1] 27 15 20 29 32 34 27 24 23 22 32 31 26 34 32 20 12 26 25 30 25 23 23 20 22
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
#> Class <disk>
#>  [1] 17 18 15 17 18 17 18 13 17 17 13 15 15 16 15 15 14 16 14 14 13 17 18 14 17
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
#> Class <disk>
#>  [1] 18 27 18 24 23 24 25 24 27 15 19 18 25 25 24 26 27 25 24 20 26 27 28 24 23
# }