update beta version to 1.8.2.*, add JSS paper

man/AMR.Rd

@@ -1,14 +1,37 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/amr.R
+\docType{package}
 \name{AMR}
 \alias{AMR}
+\alias{AMR-package}
 \title{The \code{AMR} Package}
+\source{
+To cite AMR in publications use:
+
+Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). "AMR: An R Package for Working with Antimicrobial Resistance Data." \emph{Journal of Statistical Software}, \emph{104}(3), 1-31. \doi{10.18637/jss.v104.i03}.
+
+A BibTeX entry for LaTeX users is:
+
+\preformatted{
+@Article{,
+  title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},
+  author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},
+  journal = {Journal of Statistical Software},
+  year = {2022},
+  volume = {104},
+  number = {3},
+  pages = {1--31},
+  doi = {10.18637/jss.v104.i03},
+}
+}
+}
 \description{
 Welcome to the \code{AMR} package.
-}
-\details{
+
 \code{AMR} is a free, open-source and independent \R package 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. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.
 
+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 ~49,000 distinct microbial species and all ~570 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
 
 This package is fully independent of any other \R package and works on Windows, macOS and Linux with all versions of \R since R-3.0.0 (April 2013). 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 University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This \R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
@@ -38,21 +61,43 @@ This package can be used for:
 All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, 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}.
 }
 
-\section{Contact Us}{
-
-For suggestions, comments or questions, please contact us via:
-
-Dr. Matthijs S. Berends \cr
-m.s.berends [at] umcg [dot] nl \cr
-University of Groningen
-Department of Medical Microbiology and Infection Prevention \cr
-University Medical Center Groningen \cr
-Post Office Box 30001 \cr
-9700 RB Groningen \cr
-The Netherlands
-\url{https://msberends.github.io/AMR/}
-
-If you have found a bug, please file a new issue at: \cr
-\url{https://github.com/msberends/AMR/issues}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://msberends.github.io/AMR/}
+  \item \url{https://github.com/msberends/AMR}
+  \item Report bugs at \url{https://github.com/msberends/AMR/issues}
 }
 
+}
+\author{
+\strong{Maintainer}: Matthijs S. Berends \email{m.berends@certe.nl} (\href{https://orcid.org/0000-0001-7620-1800}{ORCID})
+
+Authors:
+\itemize{
+  \item Christian F. Luz (\href{https://orcid.org/0000-0001-5809-5995}{ORCID}) [contributor]
+  \item Dennis Souverein (\href{https://orcid.org/0000-0003-0455-0336}{ORCID}) [contributor]
+  \item Erwin E. A. Hassing [contributor]
+}
+
+Other contributors:
+\itemize{
+  \item Casper J. Albers (\href{https://orcid.org/0000-0002-9213-6743}{ORCID}) [thesis advisor]
+  \item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
+  \item Judith M. Fonville [contributor]
+  \item Alex W. Friedrich (\href{https://orcid.org/0000-0003-4881-038X}{ORCID}) [thesis advisor]
+  \item Corinna Glasner (\href{https://orcid.org/0000-0003-1241-1328}{ORCID}) [thesis advisor]
+  \item Eric H. L. C. M. Hazenberg [contributor]
+  \item Gwen Knight (\href{https://orcid.org/0000-0002-7263-9896}{ORCID}) [contributor]
+  \item Annick Lenglet (\href{https://orcid.org/0000-0003-2013-8405}{ORCID}) [contributor]
+  \item Bart C. Meijer [contributor]
+  \item Dmytro Mykhailenko [contributor]
+  \item Anton Mymrikov [contributor]
+  \item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
+  \item Rogier P. Schade [contributor]
+  \item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]
+  \item Anthony Underwood (\href{https://orcid.org/0000-0002-8547-4277}{ORCID}) [contributor]
+}
+
+}
+\keyword{internal}

man/as.mo.Rd

@@ -4,7 +4,9 @@
 \alias{as.mo}
 \alias{mo}
 \alias{is.mo}
+\alias{mo_failures}
 \alias{mo_uncertainties}
+\alias{mo_renamed}
 \alias{mo_reset_session}
 \title{Transform Input to a Microorganism Code}
 \usage{
@@ -24,8 +26,12 @@ as.mo(
 
 is.mo(x)
 
+mo_failures()
+
 mo_uncertainties()
 
+mo_renamed()
+
 mo_reset_session()
 }
 \arguments{
@@ -115,7 +121,12 @@ With the default setting (\code{allow_uncertain = TRUE}, level 2), below example
 \item \code{"Fluoroquinolone-resistant Neisseria gonorrhoeae"}. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result \emph{Neisseria gonorrhoeae} (\code{B_NESSR_GNRR}) needs review.
 }
 
-Use \code{\link[=mo_uncertainties]{mo_uncertainties()}} to get a \link{data.frame} that prints in a pretty format with all taxonomic names that were guessed. The output contains the matching score for all matches (see \emph{Matching Score for Microorganisms} below).
+There are three helper functions that can be run after using the \code{\link[=as.mo]{as.mo()}} function:
+\itemize{
+\item Use \code{\link[=mo_uncertainties]{mo_uncertainties()}} to get a \link{data.frame} that prints in a pretty format with all taxonomic names that were guessed. The output contains the matching score for all matches (see \emph{Matching Score for Microorganisms} below).
+\item Use \code{\link[=mo_failures]{mo_failures()}} to get a \link{character} \link{vector} with all values that could not be coerced to a valid value.
+\item Use \code{\link[=mo_renamed]{mo_renamed()}} to get a \link{data.frame} with all values that could be coerced based on old, previously accepted taxonomic names.
+}
 }
 
 \subsection{Microbial Prevalence of Pathogens in Humans}{

man/translate.Rd

@@ -17,7 +17,7 @@ reset_AMR_locale()
 translate_AMR(x, language = get_AMR_locale())
 }
 \arguments{
-\item{language}{language to choose. Use one of these supported language names or ISO-639-1 codes: "English" ("en"), "Chinese" ("zh"), "Danish" ("da"), "Dutch" ("nl"), "French" ("fr"), "German" ("de"), "Greek" ("el"), "Italian" ("it"), "Japanese" ("ja"), "Polish" ("pl"), "Portuguese" ("pt"), "Russian" ("ru"), "Spanish" ("es"), "Swedish" ("sv"), "Turkish" ("tr"), "Ukrainian" ("uk").}
+\item{language}{language to choose. Use one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk).}
 
 \item{x}{text to translate}
 }
@@ -25,9 +25,9 @@ translate_AMR(x, language = get_AMR_locale())
 For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}} and \code{\link[=ab_name]{ab_name()}}.
 }
 \details{
-The currently 16 supported languages are English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish and Ukrainian. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
+The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
 
-\strong{To silence language notes when this package loads} on a non-English operating system, please set the option \code{AMR_locale} in your \code{.Rprofile} file like this:
+\strong{To silence language notes when this package loads} on a non-English operating system, you can set the option \code{AMR_locale} in your \code{.Rprofile} file like this:
 
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file
 utils::file.edit("~/.Rprofile")