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(v2.1.1.9060) SDD results now in as.sir()

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dr. M.S. (Matthijs) Berends
2024-06-19 15:08:23 +02:00
parent 0c3d81f32e
commit c67d003e9e
17 changed files with 34127 additions and 34129 deletions
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2
man/as.sir.Rd
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@ -214,7 +214,7 @@ After using \code{\link[=as.sir]{as.sir()}}, you can use the \code{\link[=eucast
\subsection{Machine-Readable Clinical Breakpoints}{
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 34 085 rows and 13 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 drug 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/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 34 063 rows and 14 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 drug 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/clinical_breakpoints.Rd
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@ -5,7 +5,7 @@
\alias{clinical_breakpoints}
\title{Data Set with Clinical Breakpoints for SIR Interpretation}
\format{
A \link[tibble:tibble]{tibble} with 34 085 observations and 13 variables:
A \link[tibble:tibble]{tibble} with 34 063 observations and 14 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"
@ -20,6 +20,7 @@ A \link[tibble:tibble]{tibble} with 34 085 observations and 13 variables:
\item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R"
\item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
\item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 24 breakpoints.
}
}
\usage{