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This commit is contained in:
@ -28,12 +28,12 @@ These functions are so-called '\link{Deprecated}'. They will be removed in a fut
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\section{Retired lifecycle}{
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\if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
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The \link[AMR:lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
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The \link[=lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\keyword{internal}
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@ -32,7 +32,7 @@ This package can be used for:
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\section{Contact Us}{
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@ -49,6 +49,6 @@ Post Office Box 30001 \cr
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The Netherlands
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If you have found a bug, please file a new issue at: \cr
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\url{https://gitlab.com/msberends/AMR/issues}
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\url{https://github.com/msberends/AMR/issues}
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}
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@ -20,7 +20,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
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\section{Read more on our website!}{
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||||
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\examples{
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@ -43,7 +43,7 @@ This example data set has the exact same structure as an export file from WHONET
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}
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\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
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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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\keyword{datasets}
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@ -57,12 +57,12 @@ With using \code{collapse}, this function will return a \link{character}:\cr
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\section{Maturing lifecycle}{
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\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
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The \link[AMR: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://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
|
||||
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')}.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
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}
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\examples{
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@ -79,7 +79,7 @@ The function \code{\link[=ab_url]{ab_url()}} will return the direct URL to the o
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\section{Stable lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
@ -95,7 +95,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
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|
||||
@ -24,14 +24,14 @@ Calculates age in years based on a reference date, which is the sytem date at de
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\section{Stable lifecycle}{
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||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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||||
}
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||||
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||||
\examples{
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||||
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||||
@ -36,14 +36,14 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
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\section{Stable lifecycle}{
|
||||
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||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
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||||
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@ -64,14 +64,14 @@ Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and co
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||||
These data sets are available as 'flat files' for use even without R - you can find the files here:
|
||||
\itemize{
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||||
\item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/antibiotics.txt}
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||||
\item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/antivirals.txt}
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||||
\item \url{https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt}
|
||||
\item \url{https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt}
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||||
}
|
||||
|
||||
Files in R format (with preserved data structure) can be found here:
|
||||
\itemize{
|
||||
\item \url{https://gitlab.com/msberends/AMR/raw/master/data/antibiotics.rda}
|
||||
\item \url{https://gitlab.com/msberends/AMR/raw/master/data/antivirals.rda}
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\item \url{https://github.com/msberends/AMR/raw/master/data/antibiotics.rda}
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\item \url{https://github.com/msberends/AMR/raw/master/data/antivirals.rda}
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||||
}
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||||
}
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||||
}
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@ -89,7 +89,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
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||||
\seealso{
|
||||
|
||||
@ -48,7 +48,7 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
|
||||
\section{Maturing lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
|
||||
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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||||
\section{WHOCC}{
|
||||
@ -65,7 +65,7 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -27,14 +27,14 @@ Interpret disk values as RSI values with \code{\link[=as.rsi]{as.rsi()}}. It sup
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -27,14 +27,14 @@ To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MI
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -133,7 +133,7 @@ Group 3 (least prevalent microorganisms) consists of all other microorganisms.
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
@ -148,7 +148,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -64,7 +64,7 @@ When using \code{\link[=as.rsi]{as.rsi()}} on untransformed data, the data will
|
||||
|
||||
Supported guidelines to be used as input for the \code{guideline} parameter are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020". Simply using \code{"CLSI"} or \code{"EUCAST"} for input will automatically select the latest version of that guideline.
|
||||
|
||||
The repository of this package \href{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This \strong{allows for easy implementation of these rules in laboratory information systems (LIS)}.
|
||||
The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,964 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. This \strong{allows for easy implementation of these rules in laboratory information systems (LIS)}.
|
||||
|
||||
After using \code{\link[=as.rsi]{as.rsi()}}, you can use \code{\link[=eucast_rules]{eucast_rules()}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
|
||||
|
||||
@ -88,14 +88,14 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -66,12 +66,12 @@ Abbreviations of return values when using \code{property = "U"} (unit):
|
||||
\section{Questioning lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -23,14 +23,14 @@ The function returns a \code{\link{data.frame}} with columns \code{"resistant"}
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -68,14 +68,14 @@ The language of the output can be overwritten with \code{options(AMR_locale)}, p
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -28,12 +28,12 @@ Included are:
|
||||
|
||||
The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
|
||||
|
||||
The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R}.
|
||||
The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R}.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -25,7 +25,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\seealso{
|
||||
|
||||
@ -75,7 +75,7 @@ The function \code{\link[=count_df]{count_df()}} takes any variable from \code{d
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
@ -128,7 +128,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -64,7 +64,7 @@ Before further processing, some non-EUCAST rules can be applied to improve the e
|
||||
|
||||
These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use \code{eucast_rules(..., rules = "all")}, or set the default behaviour of the \verb{[eucast_rules()]} function with \code{options(AMR.eucast_rules = "all")} (or any other valid input value(s) to the \code{rules} parameter).
|
||||
|
||||
The file containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
|
||||
The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
|
||||
}
|
||||
\section{Antibiotics}{
|
||||
|
||||
@ -156,12 +156,12 @@ The following antibiotics are used for the functions \code{\link[=eucast_rules]{
|
||||
\section{Maturing lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
|
||||
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')}.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -23,11 +23,11 @@ A \code{\link{data.frame}} with 2,000 observations and 49 variables:
|
||||
example_isolates
|
||||
}
|
||||
\description{
|
||||
A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{the tutorial on our website}.
|
||||
A data set containing 2,000 microbial isolates with their full antibiograms. The data set reflects reality and can be used to practice AMR analysis. For examples, please read \href{https://msberends.github.io/AMR/articles/AMR.html}{the tutorial on our website}.
|
||||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\keyword{datasets}
|
||||
|
||||
@ -22,7 +22,7 @@ A data set containing 3,000 microbial isolates that are not cleaned up and conse
|
||||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\keyword{datasets}
|
||||
|
||||
@ -65,7 +65,7 @@ All columns of \code{x} will be searched for known antibiotic names, abbreviatio
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
@ -125,14 +125,14 @@ A difference from I to S|R (or vice versa) means 0.5 points, a difference from S
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -100,12 +100,12 @@ If there are more than two categories and you want to find out which ones are si
|
||||
\section{Questioning lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -107,7 +107,7 @@ The colours for labels and points can be changed by adding another scale layer f
|
||||
\section{Maturing lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
|
||||
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')}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -114,7 +114,7 @@ labels_rsi_count(
|
||||
\item{...}{other parameters passed on to \code{\link[=geom_rsi]{geom_rsi()}}}
|
||||
}
|
||||
\description{
|
||||
Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \link[ggplot2:ggplot]{ggplot2} functions.
|
||||
Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on \link[ggplot2:ggplot]{ggplot2} functions.
|
||||
}
|
||||
\details{
|
||||
At default, the names of antibiotics will be shown on the plots using \code{\link[=ab_name]{ab_name()}}. This can be set with the \code{translate_ab} parameter. See \code{\link[=count_df]{count_df()}}.
|
||||
@ -124,13 +124,13 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
|
||||
|
||||
\code{\link[=facet_rsi]{facet_rsi()}} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2:facet_wrap]{ggplot2::facet_wrap()}}.
|
||||
|
||||
\code{\link[=scale_y_percent]{scale_y_percent()}} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2:scale_continuous]{ggplot2::scale_continuous()}}.
|
||||
\code{\link[=scale_y_percent]{scale_y_percent()}} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2:scale_continuous]{ggplot2::scale_y_continuous()}}.
|
||||
|
||||
\code{\link[=scale_rsi_colours]{scale_rsi_colours()}} sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using \code{\link[ggplot2:scale_brewer]{ggplot2::scale_brewer()}}.
|
||||
\code{\link[=scale_rsi_colours]{scale_rsi_colours()}} sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using \code{\link[ggplot2:scale_manual]{ggplot2::scale_fill_manual()}}.
|
||||
|
||||
\code{\link[=theme_rsi]{theme_rsi()}} is a [ggplot2 theme][\code{\link[ggplot2:theme]{ggplot2::theme()}} with minimal distraction.
|
||||
|
||||
\code{\link[=labels_rsi_count]{labels_rsi_count()}} print datalabels on the bars with percentage and amount of isolates using \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}
|
||||
\code{\link[=labels_rsi_count]{labels_rsi_count()}} print datalabels on the bars with percentage and amount of isolates using \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}.
|
||||
|
||||
\code{\link[=ggplot_rsi]{ggplot_rsi()}} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\verb{\%>\%}). See Examples.
|
||||
}
|
||||
@ -138,12 +138,12 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
|
||||
\section{Maturing lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
|
||||
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')}.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -25,12 +25,12 @@ You can look for an antibiotic (trade) name or abbreviation and it will search \
|
||||
\section{Maturing lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
|
||||
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')}.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -43,14 +43,14 @@ These functions rely on \code{\link[=merge]{merge()}}, a base R function to do j
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -109,7 +109,7 @@ The function \code{\link[=key_antibiotics_equal]{key_antibiotics_equal()}} check
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
@ -129,7 +129,7 @@ A difference from I to S|R (or vice versa) means 0.5 points, a difference from S
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -26,12 +26,12 @@ Kurtosis is a measure of the "tailedness" of the probability distribution of a r
|
||||
\section{Questioning lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\seealso{
|
||||
|
||||
@ -12,19 +12,19 @@ This page contains a section for every lifecycle (with text borrowed from the af
|
||||
\section{Experimental lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
|
||||
}
|
||||
|
||||
\section{Maturing lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
|
||||
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')}.
|
||||
}
|
||||
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
@ -32,12 +32,12 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
|
||||
\section{Retired lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{retired}. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
|
||||
}
|
||||
|
||||
\section{Questioning lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
}
|
||||
|
||||
|
||||
@ -42,14 +42,14 @@ Using RStudio? This function can also be inserted from the Addins menu and can h
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -88,14 +88,14 @@ The German national guideline - Mueller et al. (2015) Antimicrobial Resistance a
|
||||
The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)" (\href{https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH}{link})
|
||||
}
|
||||
|
||||
Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}.
|
||||
Please suggest your own (country-specific) guidelines by letting us know: \url{https://github.com/msberends/AMR/issues/new}.
|
||||
|
||||
\strong{Note:} Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named order Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu \emph{et al.} in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this \code{\link[=mdro]{mdro()}} function makes sure that results from before 2016 and after 2016 are identical.
|
||||
}
|
||||
\section{Maturing lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
|
||||
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')}.
|
||||
}
|
||||
|
||||
\section{Antibiotics}{
|
||||
@ -202,7 +202,7 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -3,9 +3,9 @@
|
||||
\docType{data}
|
||||
\name{microorganisms}
|
||||
\alias{microorganisms}
|
||||
\title{Data set with 67,108 microorganisms}
|
||||
\title{Data set with 67,150 microorganisms}
|
||||
\format{
|
||||
A \code{\link{data.frame}} with 67,108 observations and 16 variables:
|
||||
A \code{\link{data.frame}} with 67,150 observations and 16 variables:
|
||||
\itemize{
|
||||
\item \code{mo}\cr ID of microorganism as used by this package
|
||||
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}
|
||||
@ -40,18 +40,18 @@ Manually added were:
|
||||
\item 1 entry of \emph{Blastocystis} (\emph{Blastocystis hominis}), although it officially does not exist (Noel \emph{et al.} 2005, PMID 15634993)
|
||||
\item 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
|
||||
\item 6 families under the Enterobacterales order, according to Adeolu \emph{et al.} (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
|
||||
\item 7,369 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
|
||||
\item 7,411 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) since the DSMZ contain the latest taxonomic information based on recent publications
|
||||
}
|
||||
\subsection{Direct download}{
|
||||
|
||||
This data set is available as 'flat file' for use even without R - you can find the file here:
|
||||
\itemize{
|
||||
\item \url{https://gitlab.com/msberends/AMR/raw/master/data-raw/microorganisms.txt}
|
||||
\item \url{https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt}
|
||||
}
|
||||
|
||||
The file in R format (with preserved data structure) can be found here:
|
||||
\itemize{
|
||||
\item \url{https://gitlab.com/msberends/AMR/raw/master/data/microorganisms.rda}
|
||||
\item \url{https://github.com/msberends/AMR/raw/master/data/microorganisms.rda}
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -72,7 +72,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\seealso{
|
||||
|
||||
@ -27,7 +27,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\seealso{
|
||||
|
||||
@ -34,7 +34,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\seealso{
|
||||
|
||||
@ -119,7 +119,7 @@ The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the o
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
@ -144,7 +144,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -84,13 +84,13 @@ If the original Excel file is moved or deleted, the mo_source file will be remov
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
|
||||
@ -20,11 +20,11 @@ Return the symbol related to the p-value: 0 '\verb{***}' 0.001 '\verb{**}' 0.01
|
||||
\section{Questioning lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
|
||||
@ -62,7 +62,7 @@ The result of the \code{\link[=pca]{pca()}} function is a \link{prcomp} object,
|
||||
\section{Maturing lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
|
||||
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')}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -83,7 +83,7 @@ The function \code{\link[=resistance]{resistance()}} is equal to the function \c
|
||||
|
||||
\strong{Remember that you should filter your table to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set.
|
||||
|
||||
These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{\link[AMR:count]{count()}} functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can influence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} parameter).}
|
||||
These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the \code{\link[=count]{count()}} functions to count isolates. The function \code{\link[=susceptibility]{susceptibility()}} is essentially equal to \code{count_susceptible() / count_all()}. \emph{Low counts can influence the outcome - the \code{proportion} functions may camouflage this, since they only return the proportion (albeit being dependent on the \code{minimum} parameter).}
|
||||
|
||||
The function \code{\link[=proportion_df]{proportion_df()}} takes any variable from \code{data} that has an \code{\link{rsi}} class (created with \code{\link[=as.rsi]{as.rsi()}}) and calculates the proportions R, I and S. It also supports grouped variables. The function \code{\link[=rsi_df]{rsi_df()}} works exactly like \code{\link[=proportion_df]{proportion_df()}}, but adds the number of isolates.
|
||||
}
|
||||
@ -121,7 +121,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
@ -143,7 +143,7 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
@ -229,5 +229,5 @@ if (require("dplyr")) {
|
||||
}
|
||||
}
|
||||
\seealso{
|
||||
\code{\link[AMR:count]{AMR::count()}} to count resistant and susceptible isolates.
|
||||
\code{\link[=count]{count()}} to count resistant and susceptible isolates.
|
||||
}
|
||||
|
||||
@ -103,7 +103,7 @@ Valid options for the statistical model (parameter \code{model}) are:
|
||||
\section{Maturing lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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://gitlab.com/msberends/AMR/-/issues}{to suggest changes at our repository} or \link[AMR:AMR]{write us an email (see section 'Contact Us')}.
|
||||
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')}.
|
||||
}
|
||||
|
||||
\section{Interpretation of R and S/I}{
|
||||
@ -123,7 +123,7 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -26,11 +26,11 @@ rsi_translation
|
||||
Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
|
||||
}
|
||||
\details{
|
||||
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
|
||||
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
|
||||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\keyword{datasets}
|
||||
|
||||
@ -28,12 +28,12 @@ When negative: the left tail is longer; the mass of the distribution is concentr
|
||||
\section{Questioning lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
The \link[=lifecycle]{lifecycle} of this function is \strong{questioning}. This function might be no longer be optimal approach, or is it questionable whether this function should be in this \code{AMR} package at all.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\seealso{
|
||||
|
||||
@ -11,11 +11,11 @@ get_locale()
|
||||
For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}} and \code{\link[=ab_name]{ab_name()}}.
|
||||
}
|
||||
\details{
|
||||
Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv}.
|
||||
Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: \url{https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv}.
|
||||
|
||||
Currently supported languages are (besides English): Dutch, French, German, Italian, Portuguese, Spanish. Not all these languages currently have translations available for all antimicrobial agents and colloquial microorganism names.
|
||||
Currently supported languages are (besides English): Dutch, French, German, Italian, Portuguese, Spanish. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names.
|
||||
|
||||
Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion}{by creating a new issue on our repository}.
|
||||
Please suggest your own translations \href{https://github.com/msberends/AMR/issues/new?title=Translations}{by creating a new issue on our repository}.
|
||||
|
||||
This file will be read by all functions where a translated output can be desired, like all \code{\link[=mo_property]{mo_property()}} functions (\code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}}, etc.).
|
||||
|
||||
@ -24,14 +24,14 @@ The system language will be used at default, if that language is supported. The
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
||||
The \link[AMR: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.
|
||||
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, 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.
|
||||
}
|
||||
|
||||
\section{Read more on our website!}{
|
||||
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
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 analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
Reference in New Issue
Block a user