mirror of
https://github.com/msberends/AMR.git
synced 2025-07-18 02:04:42 +02:00
(v2.1.1.9228) repo cleaning
This commit is contained in:
@ -36,9 +36,13 @@ After installing this package, R knows \href{https://msberends.github.io/AMR/ref
|
||||
|
||||
The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
|
||||
}
|
||||
\section{Reference Data Publicly Available}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All data sets in this \code{AMR} package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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}.
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\seealso{
|
||||
|
||||
@ -41,9 +41,15 @@ WHONET
|
||||
\description{
|
||||
This example data set has the exact same structure as an export file from WHONET. Such files can be used with this package, as this example data set shows. The antimicrobial results are from our \link{example_isolates} data set. All patient names were created using online surname generators and are only in place for practice purposes.
|
||||
}
|
||||
\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, 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}.
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
WHONET
|
||||
}
|
||||
|
||||
@ -97,9 +97,13 @@ World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodo
|
||||
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
|
||||
}
|
||||
|
||||
\section{Reference Data Publicly Available}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All data sets in this \code{AMR} package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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}.
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -213,9 +213,13 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
|
||||
}
|
||||
}
|
||||
|
||||
\section{Reference Data Publicly Available}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All data sets in this \code{AMR} package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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}.
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -62,11 +62,16 @@ Two data sets containing all antimicrobials and antivirals. Use \code{\link[=as.
|
||||
Properties that are based on an ATC code are only available when an ATC is available. These properties are: \code{atc_group1}, \code{atc_group2}, \code{oral_ddd}, \code{oral_units}, \code{iv_ddd} and \code{iv_units}.
|
||||
|
||||
Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column \code{cid}) and consequently only available where a CID is available.
|
||||
\subsection{Direct download}{
|
||||
}
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, 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}.
|
||||
}
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\section{WHOCC}{
|
||||
|
||||
This package contains \strong{all ~550 antibiotic, antimycotic and antiviral drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://atcddd.fhi.no}) and the Pharmaceuticals Community Register of the European Commission (\url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}).
|
||||
|
||||
@ -66,9 +66,13 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
|
||||
\strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.} See \url{https://atcddd.fhi.no/copyright_disclaimer/.}
|
||||
}
|
||||
|
||||
\section{Reference Data Publicly Available}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All data sets in this \code{AMR} package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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}.
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -58,9 +58,13 @@ The WHOCC is located in Oslo at the Norwegian Institute of Public Health and fun
|
||||
\strong{NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.} See \url{https://atcddd.fhi.no/copyright_disclaimer/.}
|
||||
}
|
||||
|
||||
\section{Reference Data Publicly Available}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All data sets in this \code{AMR} package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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}.
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -202,9 +202,13 @@ When calculating the matching score, all characters in \eqn{x} and \eqn{n} are i
|
||||
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.381}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
|
||||
}
|
||||
|
||||
\section{Reference Data Publicly Available}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All data sets in this \code{AMR} package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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}.
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -256,9 +256,13 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
|
||||
}
|
||||
|
||||
\section{Reference Data Publicly Available}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All data sets in this \code{AMR} package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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}.
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -77,9 +77,13 @@ World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodo
|
||||
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
|
||||
}
|
||||
|
||||
\section{Reference Data Publicly Available}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All data sets in this \code{AMR} package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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}.
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -39,32 +39,39 @@ These breakpoints are currently implemented:
|
||||
Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
|
||||
}
|
||||
\details{
|
||||
\subsection{Different types of breakpoints}{
|
||||
\subsection{Different Types of Breakpoints}{
|
||||
|
||||
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.
|
||||
|
||||
The default is \code{"human"}, which can also be set with the 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}{
|
||||
\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 great development on the WHONET software.
|
||||
|
||||
Our import and reproduction script can be found here: \url{https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_clinical_breakpoints.R}.
|
||||
Our import and reproduction script can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/reproduction scripts/reproduction_of_clinical_breakpoints.R>.
|
||||
}
|
||||
|
||||
\subsection{Response from CLSI and EUCAST}{
|
||||
\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 (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, WHO, developers of WHONET software, and developers of this \code{AMR} package.
|
||||
}
|
||||
|
||||
\subsection{Download}{
|
||||
\subsection{Download Note}{
|
||||
|
||||
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, 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 rather complex internal methods to apply the guidelines. 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.
|
||||
This \code{AMR} package (and the WHONET software as well) contains rather complex internal methods to apply the guidelines. 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 implementing the breakpoints for own use.
|
||||
}
|
||||
}
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
clinical_breakpoints
|
||||
}
|
||||
|
||||
@ -24,9 +24,15 @@ dosage
|
||||
\description{
|
||||
EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with \code{\link[=eucast_dosage]{eucast_dosage()}}.
|
||||
}
|
||||
\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, 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}.
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
dosage
|
||||
}
|
||||
|
||||
File diff suppressed because one or more lines are too long
@ -22,9 +22,15 @@ example_isolates
|
||||
\description{
|
||||
A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read \href{https://msberends.github.io/AMR/articles/AMR.html}{the tutorial on our website}.
|
||||
}
|
||||
\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, 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}.
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
example_isolates
|
||||
}
|
||||
|
||||
@ -20,9 +20,15 @@ example_isolates_unclean
|
||||
\description{
|
||||
A data set containing 3 000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.
|
||||
}
|
||||
\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, 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}.
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
example_isolates_unclean
|
||||
}
|
||||
|
||||
@ -3,31 +3,38 @@
|
||||
\docType{data}
|
||||
\name{intrinsic_resistant}
|
||||
\alias{intrinsic_resistant}
|
||||
\title{Data Set with Bacterial Intrinsic Resistance}
|
||||
\title{Data Set Denoting Bacterial Intrinsic Resistance}
|
||||
\format{
|
||||
A \link[tibble:tibble]{tibble} with 196 665 observations and 2 variables:
|
||||
A \link[tibble:tibble]{tibble} with 271 905 observations and 2 variables:
|
||||
\itemize{
|
||||
\item \code{mo}\cr Microorganism ID
|
||||
\item \code{ab}\cr Antimicrobial ID
|
||||
\item \code{mo}\cr Microorganism ID which occurs in \code{\link[=microorganisms]{microorganisms$mo}}. Names can be retrieved using \code{\link[=mo_name]{mo_name()}}.
|
||||
\item \code{ab}\cr Antimicrobial ID which occurs in \code{\link[=antimicrobials]{antimicrobials$ab}}. Names can be retrieved using \code{\link[=ab_name]{ab_name()}}.
|
||||
}
|
||||
}
|
||||
\usage{
|
||||
intrinsic_resistant
|
||||
}
|
||||
\description{
|
||||
Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
|
||||
Data set containing 'EUCAST Expected Resistant Phenotypes' of \emph{all} bug-drug combinations between the \link{microorganisms} and \link{antimicrobials} data sets.
|
||||
}
|
||||
\details{
|
||||
This data set is based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023).
|
||||
This data set is currently based on \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023).
|
||||
|
||||
This data set is internally used by \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} (an \link[=antimicrobial_selectors]{antimicrobial selector}) and \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}
|
||||
\subsection{Direct 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, 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 \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.
|
||||
This data set is internally used by:
|
||||
\itemize{
|
||||
\item \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} (an \link[=antimicrobial_selectors]{antimicrobial selector})
|
||||
\item \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}
|
||||
}
|
||||
}
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
intrinsic_resistant
|
||||
}
|
||||
|
||||
@ -55,7 +55,7 @@ microorganisms
|
||||
\description{
|
||||
A data set containing the full microbial taxonomy (\strong{last updated: June 24th, 2024}) of six kingdoms. This data set is the backbone of this \code{AMR} package. MO codes can be looked up using \code{\link[=as.mo]{as.mo()}} and microorganism properties can be looked up using any of the \code{\link[=mo_property]{mo_*}} functions.
|
||||
|
||||
This data set is carefully crafted, yet made 100\% reproducible from public and authoritative taxonomic sources (using \href{https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R}{this script}), namely: \emph{List of Prokaryotic names with Standing in Nomenclature (LPSN)} for bacteria, \emph{MycoBank} for fungi, and \emph{Global Biodiversity Information Facility (GBIF)} for all others taxons.
|
||||
This data set is carefully crafted, yet made 100\% reproducible from public and authoritative taxonomic sources (using \link{this script}(https://github.com/msberends/AMR/blob/main/data-raw/reproduction scripts/reproduction_of_microorganisms.R)), namely: \emph{List of Prokaryotic names with Standing in Nomenclature (LPSN)} for bacteria, \emph{MycoBank} for fungi, and \emph{Global Biodiversity Information Facility (GBIF)} for all others taxons.
|
||||
}
|
||||
\details{
|
||||
Please note that entries are only based on LPSN, MycoBank, and GBIF (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.
|
||||
@ -86,13 +86,17 @@ For convenience, some entries were added manually:
|
||||
\item 8 other 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, and unknown anaerobic Gram-pos/Gram-neg bacteria)
|
||||
}
|
||||
|
||||
The syntax used to transform the original data to a cleansed \R format, can be \href{https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R}{found here}.
|
||||
The syntax used to transform the original data to a cleansed \R format, can be \link{found here}(https://github.com/msberends/AMR/blob/main/data-raw/reproduction scripts/reproduction_of_microorganisms.R).
|
||||
}
|
||||
}
|
||||
|
||||
\subsection{Direct download}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
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, 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}.
|
||||
}
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -17,9 +17,15 @@ microorganisms.codes
|
||||
\description{
|
||||
A data set containing commonly used codes for microorganisms, from laboratory systems and \href{https://whonet.org}{WHONET}. Define your own with \code{\link[=set_mo_source]{set_mo_source()}}. They will all be searched when using \code{\link[=as.mo]{as.mo()}} and consequently all the \code{\link[=mo_property]{mo_*}} functions.
|
||||
}
|
||||
\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, 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}.
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
microorganisms.codes
|
||||
|
||||
|
||||
@ -19,9 +19,15 @@ microorganisms.groups
|
||||
\description{
|
||||
A data set containing species groups and microbiological complexes, which are used in \link[=clinical_breakpoints]{the clinical breakpoints table}.
|
||||
}
|
||||
\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, 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}.
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
microorganisms.groups
|
||||
|
||||
|
||||
@ -56,9 +56,13 @@ When calculating the matching score, all characters in \eqn{x} and \eqn{n} are i
|
||||
All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., \code{"E. coli"} will return the microbial ID of \emph{Escherichia coli} (\eqn{m = 0.688}, a highly prevalent microorganism found in humans) and not \emph{Entamoeba coli} (\eqn{m = 0.381}, a less prevalent microorganism in humans), although the latter would alphabetically come first.
|
||||
}
|
||||
|
||||
\section{Reference Data Publicly Available}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All data sets in this \code{AMR} package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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}.
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
@ -227,9 +227,13 @@ This function uses \code{\link[=as.mo]{as.mo()}} internally, which uses an advan
|
||||
}
|
||||
}
|
||||
|
||||
\section{Reference Data Publicly Available}{
|
||||
\section{Download Our Reference Data}{
|
||||
|
||||
All data sets in this \code{AMR} package (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. 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}.
|
||||
All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.
|
||||
|
||||
For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.
|
||||
|
||||
Visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
|
||||
}
|
||||
|
||||
\examples{
|
||||
|
||||
Reference in New Issue
Block a user