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(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup
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@ -1,13 +1,20 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/disk.R
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\docType{data}
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\name{as.disk}
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\alias{as.disk}
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\alias{disk}
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\alias{NA_disk_}
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\alias{is.disk}
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\title{Transform Input to Disk Diffusion Diameters}
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\format{
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An object of class \code{disk} (inherits from \code{integer}) of length 1.
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}
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\usage{
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as.disk(x, na.rm = FALSE)
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NA_disk_
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is.disk(x)
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}
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\arguments{
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@ -23,6 +30,8 @@ This transforms a vector to a new class \code{\link{disk}}, which is a disk diff
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}
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\details{
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Interpret disk values as RSI values with \code{\link[=as.rsi]{as.rsi()}}. It supports guidelines from EUCAST and CLSI.
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\code{NA_disk_} is a missing value of the new \verb{<disk>} class.
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}
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\section{Stable Lifecycle}{
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@ -61,3 +70,4 @@ as.rsi(df)
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\seealso{
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\code{\link[=as.rsi]{as.rsi()}}
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}
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\keyword{datasets}
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@ -1,13 +1,20 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mic.R
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\docType{data}
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\name{as.mic}
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\alias{as.mic}
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\alias{mic}
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\alias{NA_mic_}
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\alias{is.mic}
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\title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
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\format{
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An object of class \code{mic} (inherits from \code{ordered}, \code{factor}) of length 1.
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}
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\usage{
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as.mic(x, na.rm = FALSE)
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NA_mic_
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is.mic(x)
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}
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\arguments{
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@ -19,7 +26,7 @@ is.mic(x)
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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.
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}
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\description{
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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.
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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.
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}
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\details{
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To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST and CLSI.
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@ -55,6 +62,8 @@ subset(df, x > 4) # or with dplyr: df \%>\% filter(x > 4)
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}
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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.
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\code{NA_mic_} is a missing value of the new \verb{<mic>} class.
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}
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\section{Stable Lifecycle}{
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@ -98,3 +107,4 @@ plot(mic_data, mo = "E. coli", ab = "cipro")
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\seealso{
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\code{\link[=as.rsi]{as.rsi()}}
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}
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\keyword{datasets}
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@ -1,17 +1,24 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/rsi.R
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\docType{data}
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\name{as.rsi}
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\alias{as.rsi}
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\alias{rsi}
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\alias{NA_rsi_}
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\alias{is.rsi}
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\alias{is.rsi.eligible}
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\alias{as.rsi.mic}
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\alias{as.rsi.disk}
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\alias{as.rsi.data.frame}
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\title{Interpret MIC and Disk Values, or Clean Raw R/SI Data}
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\format{
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An object of class \code{rsi} (inherits from \code{ordered}, \code{factor}) of length 1.
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}
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\usage{
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as.rsi(x, ...)
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NA_rsi_
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is.rsi(x)
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is.rsi.eligible(x, threshold = 0.05)
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@ -125,6 +132,8 @@ The function \code{\link[=is.rsi]{is.rsi()}} detects if the input contains class
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The function \code{\link[=is.rsi.eligible]{is.rsi.eligible()}} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} argument. If the input is a \link{data.frame}, it iterates over all columns and returns a \link{logical} vector.
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}
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\code{NA_rsi_} is a missing value of the new \verb{<rsi>} class.
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}
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\section{Interpretation of R and S/I}{
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@ -247,3 +256,4 @@ if (require("dplyr")) {
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\seealso{
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\code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}}, \code{\link[=as.mo]{as.mo()}}
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}
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\keyword{datasets}
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@ -100,10 +100,12 @@ It is possible to define antibiotic groups instead of single antibiotics for the
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}
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}
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\section{Maturing Lifecycle}{
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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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.
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If the unlying code needs breaking changes, they will occur gradually. For example, a argument 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.
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}
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\section{Read more on Our Website!}{
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@ -11,6 +11,7 @@
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Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
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\item EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{(link)}
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\item EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{(link)}
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\item EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf}{(link)}
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\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}{(link)}
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\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx}{(link)}
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\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. \href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx}{(link)}
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@ -24,7 +25,7 @@ eucast_rules(
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rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
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verbose = FALSE,
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version_breakpoints = 11,
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version_expertrules = 3.2,
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version_expertrules = 3.3,
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ampc_cephalosporin_resistance = NA,
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only_rsi_columns = FALSE,
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custom_rules = NULL,
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@ -46,7 +47,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
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\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "11.0" or "10.0".}
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\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.2" or "3.1".}
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\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".}
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\item{ampc_cephalosporin_resistance}{a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of \code{NA} (the default) for this argument will remove results for these three agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.}
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@ -24,10 +24,12 @@ The taxonomic names can be italicised using markdown (the default) by adding \co
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This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
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}
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\section{Maturing Lifecycle}{
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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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.
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If the unlying code needs breaking changes, they will occur gradually. For example, a argument 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.
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}
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\section{Read more on Our Website!}{
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@ -129,10 +129,12 @@ For interpreting MIC values as well as disk diffusion diameters, supported guide
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Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline.
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}
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\section{Maturing Lifecycle}{
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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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.
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If the unlying code needs breaking changes, they will occur gradually. For example, a argument 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.
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}
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\section{Read more on Our Website!}{
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