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dr. M.S. (Matthijs) Berends
2022-08-21 16:37:20 +02:00
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man/as.mic.Rd
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@ -77,44 +77,35 @@ Use \code{\link[=droplevels]{droplevels()}} to drop unused levels. At default, i
\code{NA_mic_} is a missing value of the new \verb{<mic>} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}.
}
\section{Stable Lifecycle}{
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{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, an argument will be deprecated and first continue to work, but will emit a 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.
}
\section{Read more on Our Website!}{
On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\examples{
mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
mic_data
is.mic(mic_data)
# this can also coerce combined MIC/RSI values:
as.mic("<=0.002; S") # will return <=0.002
as.mic("<=0.002; S")
# mathematical processing treats MICs as [numeric] values
# mathematical processing treats MICs as numeric values
fivenum(mic_data)
quantile(mic_data)
all(mic_data < 512)
# interpret MIC values
as.rsi(x = as.mic(2),
mo = as.mo("S. pneumoniae"),
mo = as.mo("Streptococcus pneumoniae"),
ab = "AMX",
guideline = "EUCAST")
as.rsi(x = as.mic(4),
mo = as.mo("S. pneumoniae"),
as.rsi(x = as.mic(c(0.01, 2, 4, 8)),
mo = as.mo("Streptococcus pneumoniae"),
ab = "AMX",
guideline = "EUCAST")
# plot MIC values, see ?plot
plot(mic_data)
plot(mic_data, mo = "E. coli", ab = "cipro")
autoplot(mic_data, mo = "E. coli", ab = "cipro")
autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl") # Dutch
autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "uk") # Ukrainian
}
\seealso{
\code{\link[=as.rsi]{as.rsi()}}