This transforms a vector to a new class mic, which is an ordered factor with valid minimum inhibitory concentrations (MIC) 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
To interpret MIC values as RSI values, use as.rsi() on MIC values. It supports guidelines from EUCAST and CLSI.
Stable lifecycle
The lifecycle of this function is stable. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
Read more on our website!
On our website https://msberends.github.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. As we would like to better understand the backgrounds and needs of our users, please participate in our survey!
See also
Examples
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)