P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 13:01:51 +02:00
Code Releases Activity

new species groups, updated clinical breakpoints

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-07-08 17:30:05 +02:00
parent 2d97cca6d9
commit acb534102b
172 changed files with 44445 additions and 52835 deletions
Download Patch File Download Diff File Expand all files Collapse all files

34
man/clinical_breakpoints.Rd
View File

@ -5,19 +5,19 @@
\alias{clinical_breakpoints}
\title{Data Set with Clinical Breakpoints for SIR Interpretation}
\format{
A \link[tibble:tibble]{tibble} with 42 599 observations and 12 variables:
A \link[tibble:tibble]{tibble} with 28 454 observations and 12 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{method}\cr Either "DISK" or "MIC"
\item \code{site}\cr Body site, e.g. "Oral" or "Respiratory"
\item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"
\item \code{method}\cr Testing method, either "DISK" or "MIC"
\item \code{site}\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"
\item \code{mo}\cr Microbial ID, see \code{\link[=as.mo]{as.mo()}}
\item \code{rank_index}\cr Taxonomic rank index of \code{mo} from 1 (subspecies/infraspecies) to 5 (unknown microorganism)
\item \code{ab}\cr Antibiotic ID, see \code{\link[=as.ab]{as.ab()}}
\item \code{ab}\cr Antibiotic code as used by this package, EARS-Net and WHONET, see \code{\link[=as.ab]{as.ab()}}
\item \code{ref_tbl}\cr Info about where the guideline rule can be found
\item \code{disk_dose}\cr Dose of the used disk diffusion method
\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{ecoff}\cr Epidemiological cut-off (ECOFF) value, used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi (use \code{\link[=as.sir]{as.sir(..., ecoff = TRUE)}} to interpret raw data using ECOFF values)
\item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
}
}
@ -28,11 +28,29 @@ clinical_breakpoints
Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023). Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
}
\details{
Clinical breakpoints are validated through \href{https://whonet.org}{WHONET}, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on \href{https://whonet.org}{their website}.
\subsection{Different types of breakpoints}{
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}.
Supported types of breakpoints are ECOFF, animal, and human. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.
They \strong{allow for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI.
The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}. Use \code{\link[=as.sir]{as.sir(..., breakpoint_type = ...)}} to interpret raw data using a specific breakpoint type, e.g. \code{as.sir(..., breakpoint_type = "ECOFF")} to use ECOFFs.
}
\subsection{Imported from WHONET}{
Clinical breakpoints in this package were validated through and imported from \href{https://whonet.org}{WHONET}, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on \href{https://whonet.org}{their website}. The developers of WHONET and this \code{AMR} package have been in contact about sharing their work. We highly appreciate their development on the WHONET software.
}
\subsection{Response from CLSI and EUCAST}{
The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this \code{AMR} package in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the \code{AMR} package.
}
\subsection{Download}{
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}. They allow for machine reading EUCAST and CLSI guidelines, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI, though initiatives have started to overcome these burdens.
\strong{NOTE:} this \code{AMR} package (and the WHONET software as well) contains internal methods to apply the guidelines, which is rather complex. For example, some breakpoints must be applied on certain species groups (which are in case of this package available through the \link{microorganisms.groups} data set). It is important that this is considered when using the breakpoints for own use.
}
}
\examples{
clinical_breakpoints