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Added Biometrics Template (#170)
* Added Biometrics template * Fiddling to make sure we've got the right LaTeX packages. Extended example text in template. * Added some examples and changed date to pull from Sys.Date * Added longtable * Update DESCRIPTION * Update NEWS * Update NEWS * Added biometrics_article to tests * Updated Rd and namespace using devtools::document() * Update README.md with Biometrics article * Removed dependency on tikzDevice * Added a few booktabs (for xtable compatibility) and provided command for tightlist. Changed default citation_package to natbib to match template. * changed citation_package default to "natbib"
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‎DESCRIPTION‎

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person("Dominik", "Leutnant", role = c("aut", "cph"), email = "[email protected]"),
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person(family = "MDPI", role = c("aut", "cph")),
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person("Oğuzhan", "Öğreden", role = c("aut"), comment = c(ORCID = "0000-0002-9949-3348")),
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person("Dalton", "Hance", role = c("aut"), email = "[email protected]"),
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person("Daniel", "Nüst", role = c("aut", "cph"), email = "[email protected]", comment = c(ORCID = "0000-0002-0024-5046"))
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)
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Description: A suite of custom R Markdown formats and templates for

‎NAMESPACE‎

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export(amq_article)
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export(ams_article)
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export(asa_article)
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export(biometrics_article)
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export(copernicus_article)
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export(copernicus_journal_abbreviations)
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export(ctex)

‎NEWS‎

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- Added the template for the SAGE Journals (thanks, @oguzhanogreden, #181).
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- Added the template for Biometrics (thanks, @daltonhance, #170).
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- Added the template for Copernicus Publications journals (thanks, @nuest, #172).
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- Supports syntax highlighting in the `ieee_article()` and `acm_article()` formats (thanks, @rainer-rq-koelle, #182).

‎R/biometrics_article.R‎

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#' Biometrics Journal format.
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#'
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#' This format was adapted from the Biometrics Macro package.
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#'
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#'
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#' @inheritParams rmarkdown::pdf_document
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#' @param ... Arguments to \code{rmarkdown::pdf_document}
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#' @return R Markdown output format to pass to \code{\link[rmarkdown:render]{render}}
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#' @examples
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#' \dontrun{
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#' rmarkdown::draft("MyArticle.Rmd", template = "biometrics_article", package = "rticles")
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#' }
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#'
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#' @export
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biometrics_article <- function(..., keep_tex = TRUE, citation_package = 'natbib'){
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template <- find_resource("biometrics_article", "template.tex")
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inherit_pdf_document(template = template,
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keep_tex = keep_tex,
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citation_package = citation_package,
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...)
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}

‎README.md‎

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- [AMS](https://www.ametsoc.org/) articles
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- [Biometrics](http://www.biometrics.tibs.org/) articles
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- [Bulletin de l'AMQ](https://www.amq.math.ca/bulletin/) journal submissions
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- [CTeX](http://ctex.org) documents

‎inst/rmarkdown/templates/biometrics_article/resources/template.tex‎

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\documentclass[useAMS,usenatbib$if(referee)$,referee$endif$]{biom}
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%\documentclass[useAMS,usenatbib,referee]{biom}
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%
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%
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% Papers submitted to Biometrics should ALWAYS be prepared
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% using the referee option!!!!
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%
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%
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% If your system does not have the AMS fonts version 2.0 installed, then
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% remove the useAMS option.
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%
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% useAMS allows you to obtain upright Greek characters.
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% e.g. \umu, \upi etc. See the section on "Upright Greek characters" in
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% this guide for further information.
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%
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% If you are using AMS 2.0 fonts, bold math letters/symbols are available
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% at a larger range of sizes for NFSS release 1 and 2 (using \boldmath or
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% preferably \bmath).
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%
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% The usenatbib command allows the use of Patrick Daly's natbib package for
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% cross-referencing.
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%
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% If you wish to typeset the paper in Times font (if you do not have the
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% PostScript Type 1 Computer Modern fonts you will need to do this to get
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% smoother fonts in a PDF file) then uncomment the next line
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% \usepackage{Times}
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%%%%% AUTHORS - PLACE YOUR OWN MACROS HERE %%%%%
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\usepackage[figuresright]{rotating}
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\usepackage{tikz}
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\usepackage{amsmath}
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\usepackage[hyphens]{url} % not crucial - just used below for the URL
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\usepackage{hyperref}
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\usepackage[utf8]{inputenc}
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\usepackage{graphicx}
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\usepackage{longtable}
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\usepackage{booktabs}
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%% \raggedbottom % To avoid glue in typesetteing, sbs>>
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$if(highlighting-macros)$
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$highlighting-macros$
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$endif$
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% tightlist command for lists without linebreak
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\providecommand{\tightlist}{%
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\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\setcounter{footnote}{2}
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\title[$header$]{$title$}
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\author{$for(author)$ $author.name$ \email{$author.email$} \\ $author.affiliation$ $sep$ \and
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$endfor$
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}
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\begin{document}
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\date{{\it Received $month$} $year$}
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\pagerange{\pageref{firstpage}--\pageref{lastpage}} \pubyear{$year$}
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\volume{0}
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\artmonth{January}
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\doi{0000-0000-0000}
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% This label and the label ``lastpage'' are used by the \pagerange
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% command above to give the page range for the article
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\label{firstpage}
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% pub the summary here
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\begin{abstract}
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$abstract$
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\end{abstract}
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%
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% Please place your key words in alphabetical order, separated
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% by semicolons, with the first letter of the first word capitalized,
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% and a period at the end of the list.
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%
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\begin{keywords}
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$keywords$.
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\end{keywords}
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\maketitle
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$body$
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$if(natbib)$
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\bibliographystyle{biom}
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\bibliography{$bibliography$}
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$endif$
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\label{lastpage}
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\end{document}

‎inst/rmarkdown/templates/biometrics_article/skeleton/bibliography.bib‎

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%% This BibTeX bibliography file was created using BibDesk.
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%% http://bibdesk.sourceforge.net/
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%% Created for Sachs, Michael (NIH/NCI) [E] at 2014-10-27 13:53:44 -0400
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%% Saved with string encoding Unicode (UTF-8)
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@book{pepe2003statistical,
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Author = {Pepe, Margaret Sullivan},
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Date-Added = {2014-10-27 17:28:41 +0000},
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Date-Modified = {2014-10-27 17:53:38 +0000},
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Publisher = {Oxford University Press},
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Title = {The statistical evaluation of medical tests for classification and prediction},
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Year = {2003}}
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@article{hoerl1970ridge,
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Author = {Hoerl, Arthur E and Kennard, Robert W},
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Date-Added = {2014-10-27 17:28:25 +0000},
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Date-Modified = {2014-10-27 17:28:25 +0000},
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Journal = {Technometrics},
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Number = {1},
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Pages = {55--67},
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Publisher = {Taylor \& Francis Group},
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Title = {Ridge regression: Biased estimation for nonorthogonal problems},
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Volume = {12},
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Year = {1970}}
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@article{zou2005regularization,
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Author = {Zou, Hui and Hastie, Trevor},
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Date-Added = {2014-10-27 17:28:23 +0000},
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Date-Modified = {2014-10-27 17:28:23 +0000},
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Journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
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Number = {2},
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Pages = {301--320},
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Publisher = {Blackwell Publishing Ltd},
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Title = {Regularization and variable selection via the elastic net},
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Volume = {67},
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Year = {2005}}
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@article{schoenfeld1982partial,
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Author = {Schoenfeld, David},
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Date-Added = {2014-10-27 17:28:09 +0000},
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Date-Modified = {2014-10-27 17:28:09 +0000},
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Journal = {Biometrika},
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Number = {1},
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Pages = {239--241},
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Publisher = {Oxford University Press},
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Title = {Partial residuals for the proportional hazards regression model},
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Volume = {69},
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Year = {1982}}
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@article{heagerty2000time,
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Author = {Heagerty, Patrick J and Lumley, Thomas and Pepe, Margaret S},
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Date-Added = {2014-10-27 17:28:02 +0000},
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Date-Modified = {2014-10-27 17:28:02 +0000},
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Journal = {Biometrics},
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Number = {2},
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Pages = {337--344},
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Publisher = {Blackwell Publishing Ltd},
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Title = {Time-dependent ROC curves for censored survival data and a diagnostic marker},
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Volume = {56},
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Year = {2000}}

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