(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup

man/as.mic.Rd

@@ -1,13 +1,20 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/mic.R
+\docType{data}
 \name{as.mic}
 \alias{as.mic}
 \alias{mic}
+\alias{NA_mic_}
 \alias{is.mic}
 \title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
+\format{
+An object of class \code{mic} (inherits from \code{ordered}, \code{factor}) of length 1.
+}
 \usage{
 as.mic(x, na.rm = FALSE)
 
+NA_mic_
+
 is.mic(x)
 }
 \arguments{
@@ -19,7 +26,7 @@ is.mic(x)
 Ordered \link{factor} with additional class \code{\link{mic}}, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a \link{numeric} value.
 }
 \description{
-This ransforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
+This transforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
 }
 \details{
 To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST and CLSI.
@@ -55,6 +62,8 @@ subset(df, x > 4) # or with dplyr: df \%>\% filter(x > 4)
 }
 
 The following \link[=groupGeneric]{generic functions} are implemented for the MIC class: \code{!}, \code{!=}, \code{\%\%}, \code{\%/\%}, \code{&}, \code{*}, \code{+}, \code{-}, \code{/}, \code{<}, \code{<=}, \code{==}, \code{>}, \code{>=}, \code{^}, \code{|}, \code{\link[=abs]{abs()}}, \code{\link[=acos]{acos()}}, \code{\link[=acosh]{acosh()}}, \code{\link[=all]{all()}}, \code{\link[=any]{any()}}, \code{\link[=asin]{asin()}}, \code{\link[=asinh]{asinh()}}, \code{\link[=atan]{atan()}}, \code{\link[=atanh]{atanh()}}, \code{\link[=ceiling]{ceiling()}}, \code{\link[=cos]{cos()}}, \code{\link[=cosh]{cosh()}}, \code{\link[=cospi]{cospi()}}, \code{\link[=cummax]{cummax()}}, \code{\link[=cummin]{cummin()}}, \code{\link[=cumprod]{cumprod()}}, \code{\link[=cumsum]{cumsum()}}, \code{\link[=digamma]{digamma()}}, \code{\link[=exp]{exp()}}, \code{\link[=expm1]{expm1()}}, \code{\link[=floor]{floor()}}, \code{\link[=gamma]{gamma()}}, \code{\link[=lgamma]{lgamma()}}, \code{\link[=log]{log()}}, \code{\link[=log1p]{log1p()}}, \code{\link[=log2]{log2()}}, \code{\link[=log10]{log10()}}, \code{\link[=max]{max()}}, \code{\link[=mean]{mean()}}, \code{\link[=min]{min()}}, \code{\link[=prod]{prod()}}, \code{\link[=range]{range()}}, \code{\link[=round]{round()}}, \code{\link[=sign]{sign()}}, \code{\link[=signif]{signif()}}, \code{\link[=sin]{sin()}}, \code{\link[=sinh]{sinh()}}, \code{\link[=sinpi]{sinpi()}}, \code{\link[=sqrt]{sqrt()}}, \code{\link[=sum]{sum()}}, \code{\link[=tan]{tan()}}, \code{\link[=tanh]{tanh()}}, \code{\link[=tanpi]{tanpi()}}, \code{\link[=trigamma]{trigamma()}} and \code{\link[=trunc]{trunc()}}. Some functions of the \code{stats} package are also implemented: \code{\link[=median]{median()}}, \code{\link[=quantile]{quantile()}}, \code{\link[=mad]{mad()}}, \code{\link[=IQR]{IQR()}}, \code{\link[=fivenum]{fivenum()}}. Also, \code{\link[=boxplot.stats]{boxplot.stats()}} is supported. Since \code{\link[=sd]{sd()}} and \code{\link[=var]{var()}} are non-generic functions, these could not be extended. Use \code{\link[=mad]{mad()}} as an alternative, or use e.g. \code{sd(as.numeric(x))} where \code{x} is your vector of MIC values.
+
+\code{NA_mic_} is a missing value of the new \verb{<mic>} class.
 }
 \section{Stable Lifecycle}{
 
@@ -98,3 +107,4 @@ plot(mic_data, mo = "E. coli", ab = "cipro")
 \seealso{
 \code{\link[=as.rsi]{as.rsi()}}
 }
+\keyword{datasets}