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MO group fixes

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dr. M.S. (Matthijs) Berends
2023-07-12 15:04:48 +01:00
parent 9cf054903b
commit 0c46f61260
28 changed files with 1822 additions and 861 deletions
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2
man/as.sir.Rd
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@@ -171,7 +171,7 @@ 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 28 885 rows and 12 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 29 747 rows and 12 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}{

2
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 28 885 observations and 12 variables:
A \link[tibble:tibble]{tibble} with 29 747 observations and 12 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"

4
man/microorganisms.groups.Rd
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@@ -3,9 +3,9 @@
\docType{data}
\name{microorganisms.groups}
\alias{microorganisms.groups}
\title{Data Set with 448 Microorganisms In Species Groups}
\title{Data Set with 507 Microorganisms In Species Groups}
\format{
A \link[tibble:tibble]{tibble} with 448 observations and 4 variables:
A \link[tibble:tibble]{tibble} with 507 observations and 4 variables:
\itemize{
\item \code{mo_group}\cr ID of the species group / microbiological complex
\item \code{mo}\cr ID of the microorganism belonging in the species group / microbiological complex