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new rsi_translation

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dr. M.S. (Matthijs) Berends
2022-10-22 22:00:15 +02:00
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2
man/AMR.Rd
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@ -39,7 +39,7 @@ This package is fully independent of any other \R package and works on Windows,
This package can be used for:
\itemize{
\item Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF)
\item Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
\item Interpreting raw MIC and disk diffusion values, based on any CLSI or EUCAST guideline from the last 10 years
\item Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
\item Determining first isolates to be used for AMR data analysis
\item Calculating antimicrobial resistance

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man/as.mic.Rd
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@ -33,7 +33,7 @@ Ordered \link{factor} with additional class \code{\link{mic}}, that in mathemati
This transforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
}
\details{
To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST (2011-2022) and CLSI (2011-2022).
To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST (2013-2022) and CLSI (2013-2022).
This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:

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man/as.rsi.Rd
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@ -15,6 +15,14 @@
\format{
An object of class \code{rsi} (inherits from \code{ordered}, \code{factor}) of length 1.
}
\source{
For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
\itemize{
\item \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data}, 2013-2022, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
\item \strong{M100 Performance Standard for Antimicrobial Susceptibility Testing}, 2013-2022, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
\item \strong{Breakpoint tables for interpretation of MICs and zone diameters}, 2013-2022, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
}
}
\usage{
as.rsi(x, ...)
@ -71,7 +79,7 @@ rsi_interpretation_history(clean = FALSE)
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{rsi_translation} data set), supports EUCAST (2011-2022) and CLSI (2011-2022), see \emph{Details}}
\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{rsi_translation} data set), supports EUCAST (2013-2022) and CLSI (2013-2022), see \emph{Details}}
\item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.rsi]{as.rsi()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
@ -122,7 +130,7 @@ For points 2, 3 and 4: Use \code{\link[=rsi_interpretation_history]{rsi_interpre
\subsection{Supported Guidelines}{
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022).
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022).
Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2022"} or \code{"CLSI 2022"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
}
@ -134,7 +142,7 @@ After using \code{\link[=as.rsi]{as.rsi()}}, you can use the \code{\link[=eucast
\subsection{Machine-Readable Interpretation Guidelines}{
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 20,369 rows and 11 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. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 18,308 rows and 11 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. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
}
\subsection{Other}{

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man/bug_drug_combinations.Rd
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@ -4,9 +4,6 @@
\alias{bug_drug_combinations}
\alias{format.bug_drug_combinations}
\title{Determine Bug-Drug Combinations}
\source{
\strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition}, 2022, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
}
\usage{
bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)

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man/microorganisms.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data Set with 48,787 Microorganisms}
\title{Data Set with 48,788 Microorganisms}
\format{
A \link[tibble:tibble]{tibble} with 48,787 observations and 22 variables:
A \link[tibble:tibble]{tibble} with 48,788 observations and 22 variables:
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.

4
man/microorganisms.codes.Rd
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@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms.codes}
\alias{microorganisms.codes}
\title{Data Set with 5,411 Common Microorganism Codes}
\title{Data Set with 5,932 Common Microorganism Codes}
\format{
A \link[tibble:tibble]{tibble} with 5,411 observations and 2 variables:
A \link[tibble:tibble]{tibble} with 5,932 observations and 2 variables:
\itemize{
\item \code{code}\cr Commonly used code of a microorganism
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set

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man/plot.Rd
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@ -126,7 +126,7 @@ Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support f
\details{
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012" and "CLSI 2011".
For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014" and "CLSI 2013".
Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline.
}

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man/rsi_translation.Rd
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@ -5,7 +5,7 @@
\alias{rsi_translation}
\title{Data Set for R/SI Interpretation}
\format{
A \link[tibble:tibble]{tibble} with 20,369 observations and 11 variables:
A \link[tibble:tibble]{tibble} with 18,308 observations and 11 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{method}\cr Either "DISK" or "MIC"
@ -24,7 +24,7 @@ A \link[tibble:tibble]{tibble} with 20,369 observations and 11 variables:
rsi_translation
}
\description{
Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
}
\details{
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.