Class 'mic'

This transforms a vector to a new class mic, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as NA with a warning.

as.mic(x, na.rm = FALSE)

is.mic(x)

Arguments

x	vector
na.rm	a logical indicating whether missing values should be removed

Value

Ordered factor with new class mic

Details

Interpret MIC values as RSI values with as.rsi. It supports guidelines from EUCAST and CLSI.

Read more on our website!

On our website https://msberends.gitlab.io/AMR you can find a comprehensive tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.

See also

as.rsi

Examples

# NOT RUN {
mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
is.mic(mic_data)

# this can also coerce combined MIC/RSI values:
as.mic("<=0.002; S") # will return <=0.002

# interpret MIC values
as.rsi(x = as.mic(2),
       mo = as.mo("S. pneumoniae"),
       ab = "AMX",
       guideline = "EUCAST")
as.rsi(x = as.mic(4),
       mo = as.mo("S. pneumoniae"),
       ab = "AMX",
       guideline = "EUCAST")

plot(mic_data)
barplot(mic_data)
freq(mic_data)
# }