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8
man/AMR.Rd
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@ -28,11 +28,11 @@ A BibTeX entry for LaTeX users is:
\description{
Welcome to the \code{AMR} package.
The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://msberends.github.io/AMR/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!
The \code{AMR} package is a \href{https://amr-for-r.org/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://amr-for-r.org/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!
This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://msberends.github.io/AMR/reference/antimicrobials.html}{\strong{~620 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
After installing this package, R knows \href{https://amr-for-r.org/reference/microorganisms.html}{\strong{~79 000 microorganisms}} (updated June 2024) and all \href{https://amr-for-r.org/reference/antimicrobials.html}{\strong{~620 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the public \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
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.
}
@ -42,13 +42,13 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{
Useful links:
\itemize{
\item \url{https://msberends.github.io/AMR/}
\item \url{https://www.amr-for-r.org/}
\item \url{https://github.com/msberends/AMR}
\item Report bugs at \url{https://github.com/msberends/AMR/issues}
}

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man/WHONET.Rd
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@ -47,7 +47,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

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man/ab_property.Rd
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@ -103,7 +103,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

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man/antimicrobial_selectors.Rd
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@ -163,7 +163,7 @@ my_data_with_all_these_columns \%>\%
\details{
These functions can be used in data set calls for selecting columns and filtering rows. They work with base \R, the Tidyverse, and \code{data.table}. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but are not limited to \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}.
All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling.
All selectors can also be used in \code{tidymodels} packages such as \code{recipe} and \code{parsnip}. See for more info \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{our tutorial} on using antimicrobial selectors for predictive modelling.
All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the \link{antimicrobials} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
@ -219,7 +219,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

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man/antimicrobials.Rd
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@ -69,7 +69,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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}{

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man/as.ab.Rd
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@ -72,7 +72,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/as.av.Rd
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@ -64,7 +64,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/as.mo.Rd
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@ -208,7 +208,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

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man/as.sir.Rd
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@ -12,7 +12,7 @@
\alias{as.sir.disk}
\alias{as.sir.data.frame}
\alias{sir_interpretation_history}
\title{Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data}
\title{Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data}
\source{
For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
\itemize{
@ -20,7 +20,7 @@ For interpretations of minimum inhibitory concentration (MIC) values and disk di
\item \strong{CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing}, 2011-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/microbiology/documents/m100/}.
\item \strong{CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals}, 2019-2024, \emph{Clinical and Laboratory Standards Institute} (CLSI). \url{https://clsi.org/standards/products/veterinary-medicine/documents/vet01/}.
\item \strong{EUCAST Breakpoint tables for interpretation of MICs and zone diameters}, 2011-2024, \emph{European Committee on Antimicrobial Susceptibility Testing} (EUCAST). \url{https://www.eucast.org/clinical_breakpoints}.
\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://msberends.github.io/AMR/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
\item \strong{WHONET} as a source for machine-reading the clinical breakpoints (\href{https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet}{read more here}), 1989-2024, \emph{WHO Collaborating Centre for Surveillance of Antimicrobial Resistance}. \url{https://whonet.org/}.
}
}
\usage{
@ -247,7 +247,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/av_property.Rd
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@ -83,7 +83,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/clinical_breakpoints.Rd
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@ -69,7 +69,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/dosage.Rd
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@ -30,7 +30,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/eucast_rules.Rd
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@ -111,7 +111,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

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man/example_isolates.Rd
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@ -20,7 +20,7 @@ A \link[tibble:tibble]{tibble} with 2 000 observations and 46 variables:
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}.
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://amr-for-r.org/articles/AMR.html}{the tutorial on our website}.
}
\section{Download Our Reference Data}{
@ -28,7 +28,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/example_isolates_unclean.Rd
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@ -26,7 +26,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/intrinsic_resistant.Rd
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@ -32,7 +32,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/microorganisms.Rd
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@ -96,7 +96,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/microorganisms.codes.Rd
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@ -23,7 +23,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/microorganisms.groups.Rd
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@ -25,7 +25,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/mo_matching_score.Rd
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@ -62,7 +62,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{

2
man/mo_property.Rd
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@ -233,7 +233,7 @@ All reference data sets in the AMR package - including information on microorgan
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}.
Visit \href{https://amr-for-r.org/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{