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"

DESCRIPTION

@@ -28,6 +28,7 @@ Authors@R: c(
   person("Dominik", "Leutnant", role = c("aut", "cph"), email = "leutnant@fh-muenster.de"),
   person(family = "MDPI", role = c("aut", "cph")),
   person("Oğuzhan", "Öğreden", role = c("aut"), comment = c(ORCID = "0000-0002-9949-3348")),
+  person("Dalton", "Hance", role = c("aut"), email = "dhance@usgs.gov"),
   person("Daniel", "Nüst", role = c("aut", "cph"), email = "daniel.nuest@uni-muenster.de", comment = c(ORCID = "0000-0002-0024-5046"))
   )
 Description: A suite of custom R Markdown formats and templates for

NAMESPACE

@@ -6,6 +6,7 @@ export(aea_article)
 export(amq_article)
 export(ams_article)
 export(asa_article)
+export(biometrics_article)
 export(copernicus_article)
 export(copernicus_journal_abbreviations)
 export(ctex)

NEWS

@@ -3,6 +3,8 @@ rticles 0.6 (unreleased)
 
 - Added the template for the SAGE Journals (thanks, @oguzhanogreden, #181).
 
+- Added the template for Biometrics (thanks, @daltonhance, #170).
+
 - Added the template for Copernicus Publications journals (thanks, @nuest, #172).
 
 - Supports syntax highlighting in the `ieee_article()` and `acm_article()` formats (thanks, @rainer-rq-koelle, #182).

R/biometrics_article.R

@@ -0,0 +1,21 @@
+#' Biometrics Journal format.
+#'
+#' This format was adapted from the Biometrics Macro package.
+#'
+#'
+#' @inheritParams rmarkdown::pdf_document
+#' @param ... Arguments to \code{rmarkdown::pdf_document}
+#' @return R Markdown output format to pass to \code{\link[rmarkdown:render]{render}}
+#' @examples
+#' \dontrun{
+#' rmarkdown::draft("MyArticle.Rmd", template = "biometrics_article", package = "rticles")
+#' }
+#'
+#' @export
+biometrics_article <- function(..., keep_tex = TRUE, citation_package = 'natbib'){
+  template <- find_resource("biometrics_article", "template.tex")
+  inherit_pdf_document(template = template,
+                              keep_tex = keep_tex,
+                              citation_package = citation_package,
+                              ...)
+}

README.md

@@ -26,6 +26,8 @@ The **rticles** package provides a suite of custom [R Markdown](http://rmarkdown
 
 - [AMS](https://www.ametsoc.org/) articles
 
+- [Biometrics](http://www.biometrics.tibs.org/) articles
+
 - [Bulletin de l'AMQ](https://www.amq.math.ca/bulletin/) journal submissions
 
 - [CTeX](http://ctex.org) documents

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

@@ -0,0 +1,101 @@
+\documentclass[useAMS,usenatbib$if(referee)$,referee$endif$]{biom}
+%\documentclass[useAMS,usenatbib,referee]{biom}
+%
+%
+%  Papers submitted to Biometrics should ALWAYS be prepared
+%  using the referee option!!!!
+%
+%
+% If your system does not have the AMS fonts version 2.0 installed, then
+% remove the useAMS option.
+%
+% useAMS allows you to obtain upright Greek characters.
+% e.g. \umu, \upi etc.  See the section on "Upright Greek characters" in
+% this guide for further information.
+%
+% If you are using AMS 2.0 fonts, bold math letters/symbols are available
+% at a larger range of sizes for NFSS release 1 and 2 (using \boldmath or
+% preferably \bmath).
+%
+% The usenatbib command allows the use of Patrick Daly's natbib package for
+% cross-referencing.
+%
+% If you wish to typeset the paper in Times font (if you do not have the
+% PostScript Type 1 Computer Modern fonts you will need to do this to get
+% smoother fonts in a PDF file) then uncomment the next line
+% \usepackage{Times}
+%%%%% AUTHORS - PLACE YOUR OWN MACROS HERE %%%%%
+
+\usepackage[figuresright]{rotating}
+\usepackage{tikz}
+\usepackage{amsmath}
+\usepackage[hyphens]{url} % not crucial - just used below for the URL
+\usepackage{hyperref}
+\usepackage[utf8]{inputenc}
+\usepackage{graphicx}
+\usepackage{longtable}
+\usepackage{booktabs}
+%% \raggedbottom % To avoid glue in typesetteing, sbs>>
+
+$if(highlighting-macros)$
+$highlighting-macros$
+$endif$
+
+% tightlist command for lists without linebreak
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\setcounter{footnote}{2}
+
+\title[$header$]{$title$}
+
+\author{$for(author)$ $author.name$ \email{$author.email$} \\ $author.affiliation$ $sep$ \and
+		$endfor$
+	   }
+
+\begin{document}
+
+\date{{\it Received $month$} $year$}
+
+\pagerange{\pageref{firstpage}--\pageref{lastpage}} \pubyear{$year$}
+
+\volume{0}
+\artmonth{January}
+\doi{0000-0000-0000}
+
+%  This label and the label ``lastpage'' are used by the \pagerange
+%  command above to give the page range for the article
+
+\label{firstpage}
+
+%  pub the summary here
+
+\begin{abstract}
+$abstract$
+\end{abstract}
+
+%
+%  Please place your key words in alphabetical order, separated
+%  by semicolons, with the first letter of the first word capitalized,
+%  and a period at the end of the list.
+%
+
+\begin{keywords}
+$keywords$.
+\end{keywords}
+
+\maketitle
+
+$body$
+
+$if(natbib)$
+
+\bibliographystyle{biom}
+\bibliography{$bibliography$}
+
+$endif$
+
+\label{lastpage}
+
+\end{document}

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

@@ -0,0 +1,66 @@
+%% This BibTeX bibliography file was created using BibDesk.
+%% http://bibdesk.sourceforge.net/
+
+
+%% Created for Sachs, Michael (NIH/NCI) [E] at 2014-10-27 13:53:44 -0400 
+
+
+%% Saved with string encoding Unicode (UTF-8) 
+
+
+
+@book{pepe2003statistical,
+	Author = {Pepe, Margaret Sullivan},
+	Date-Added = {2014-10-27 17:28:41 +0000},
+	Date-Modified = {2014-10-27 17:53:38 +0000},
+	Publisher = {Oxford University Press},
+	Title = {The statistical evaluation of medical tests for classification and prediction},
+	Year = {2003}}
+
+@article{hoerl1970ridge,
+	Author = {Hoerl, Arthur E and Kennard, Robert W},
+	Date-Added = {2014-10-27 17:28:25 +0000},
+	Date-Modified = {2014-10-27 17:28:25 +0000},
+	Journal = {Technometrics},
+	Number = {1},
+	Pages = {55--67},
+	Publisher = {Taylor \& Francis Group},
+	Title = {Ridge regression: Biased estimation for nonorthogonal problems},
+	Volume = {12},
+	Year = {1970}}
+
+@article{zou2005regularization,
+	Author = {Zou, Hui and Hastie, Trevor},
+	Date-Added = {2014-10-27 17:28:23 +0000},
+	Date-Modified = {2014-10-27 17:28:23 +0000},
+	Journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
+	Number = {2},
+	Pages = {301--320},
+	Publisher = {Blackwell Publishing Ltd},
+	Title = {Regularization and variable selection via the elastic net},
+	Volume = {67},
+	Year = {2005}}
+
+@article{schoenfeld1982partial,
+	Author = {Schoenfeld, David},
+	Date-Added = {2014-10-27 17:28:09 +0000},
+	Date-Modified = {2014-10-27 17:28:09 +0000},
+	Journal = {Biometrika},
+	Number = {1},
+	Pages = {239--241},
+	Publisher = {Oxford University Press},
+	Title = {Partial residuals for the proportional hazards regression model},
+	Volume = {69},
+	Year = {1982}}
+
+@article{heagerty2000time,
+	Author = {Heagerty, Patrick J and Lumley, Thomas and Pepe, Margaret S},
+	Date-Added = {2014-10-27 17:28:02 +0000},
+	Date-Modified = {2014-10-27 17:28:02 +0000},
+	Journal = {Biometrics},
+	Number = {2},
+	Pages = {337--344},
+	Publisher = {Blackwell Publishing Ltd},
+	Title = {Time-dependent ROC curves for censored survival data and a diagnostic marker},
+	Volume = {56},
+	Year = {2000}}