Add new article template for Bioinformatics (#297)

* Create bioinformatics journal

* Remove useless files & follow PR templates

* Update based on Yihui's suggestions

* Fix description error

* Delete bioinformatics.csl

* file has been deleted so unnecessary

* already set in the template file

* missing new line

* devtools::document()

* add contributors in NEWS.md

* order format alphabetically

* resolve conflict on README

* resolve conflict with test file

Co-authored-by: Christophe Dervieux <cderv@rstudio.com>

.gitignore

@@ -2,3 +2,4 @@
 .Rproj.user
 .Rhistory
 .RData
+*.log

DESCRIPTION

@@ -40,6 +40,8 @@ Authors@R: c(
   person("Robrecht", "Cannoodt", role = c("aut", "cph"), email = "rcannood@gmail.com", comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood")),
   person("Duncan", "Luguern", role = c("aut"), email = "duncan.luguern@gmail.com"),
   person("David M.", "Kaplan", role = c("aut", "ctb"), email = "dmkaplan2000@gmail.com", comment = c(ORCID = "0000-0001-6087-359X", github = "dmkaplan2000")),
+  person("Shixiang", "Wang", role = c("aut", "ctb"), email = "w_shixiang@163.com", comment = c(ORCID = "0000-0001-9855-7357")),
+  person('Jay', 'Hesselberth', role = c('aut', 'ctb'), email = 'jay.hesselberth@gmail.com', comment = c(ORCID = '0000-0002-6299-179X')),
   person("Alfredo", "Hernández", role = c("ctb"), email = "aldomann.designs@gmail.com", comment = c(ORCID = "0000-0002-2660-4545"))
   )
 Description: A suite of custom R Markdown formats and templates for
@@ -49,6 +51,6 @@ Imports: utils, rmarkdown, knitr, yaml, tinytex (>= 0.19), xfun
 SystemRequirements: GNU make
 URL: https://github.com/rstudio/rticles
 BugReports: https://github.com/rstudio/rticles/issues
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.1
 Suggests: testit, bookdown, xtable
 Encoding: UTF-8

NAMESPACE

@@ -8,6 +8,7 @@ export(amq_article)
 export(ams_article)
 export(arxiv_article)
 export(asa_article)
+export(bioinformatics_article)
 export(biometrics_article)
 export(copernicus_article)
 export(copernicus_journal_abbreviations)

NEWS.md

@@ -1,6 +1,9 @@
 rticles 0.15
 ---------------------------------------------------------------------
 
+
+- Added article template for journal *Bioinformatics*. (thanks, @ShixiangWang, #297)
+
 - Update Copernicus Publications template to version 5.8 (thanks, @nuest, #274).
 
 - Fixed issue with multi-line authors on JSS template when using `\AND`, which was firstly implemented in b740b19b90cd6f7afe2cd7d66456c9efa0bb4cdf (thanks, @aldomann, #292).

R/article.R

@@ -115,6 +115,17 @@ arxiv_article <- function(..., keep_tex = TRUE) {
   )
 }
 
+#' @section \code{bioinformatics_article}: Format for creating submissions to a Bioinformatics journal. Adapted from
+#' \url{https://academic.oup.com/bioinformatics/pages/submission_online}.
+#' @export
+#' @rdname article
+bioinformatics_article <- function(..., keep_tex = TRUE, citation_package = 'natbib') {
+  pdf_document_format(
+    "bioinformatics_article", keep_tex = keep_tex, citation_package = citation_package,
+    md_extensions = "-auto_identifiers",...
+  )
+}
+
 #' @section \code{biometrics_article}: This format was adapted from the
 #'   Biometrics journal.
 #' @export

README.md

@@ -27,6 +27,7 @@ The **rticles** package provides a suite of custom [R Markdown](http://rmarkdown
 | [AMS: American Meteorological Society](https://www.ametsoc.org/) | [@yufree](https://github.com/yufree) | [#96](https://github.com/rstudio/rticles/pull/96) | `ams_article()` |
 | [ASA: American Statistical Association](https://www.amstat.org/) |  | [#111](https://github.com/rstudio/rticles/pull/111) | `asa_article()` |
 | [arXiv](https://arxiv.org/) pre-prints based on George Kour's template | [@alexpghayes](https://github.com) | [#236](https://github.com/rstudio/rticles/pull/236) | `arxiv_article()` |
+| [Bioinformatics](https://academic.oup.com/bioinformatics) | [@ShixiangWang](https://github.com/ShixiangWang) | [#297](https://github.com/rstudio/rticles/pull/297) | `bioinformatics_article()` |
 | [Biometrics](http://www.biometrics.tibs.org/) | [@daltonhance](https://github.com/daltonhance) | [#170](https://github.com/rstudio/rticles/pull/170) | `biometrics_article()` |
 | [Bulletin de l'AMQ](https://www.amq.math.ca/bulletin/) | [@desautm](https://github.com/desautm) | [#145](https://github.com/rstudio/rticles/pull/145) | `amq_article()` |
 | [Copernicus Publications](https://publications.copernicus.org) | [@nuest](https://github.com/nuest) | [#172](https://github.com/rstudio/rticles/pull/172) | `copernicus_article()` |

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

@@ -0,0 +1,68 @@
+\documentclass{bioinfo}
+\copyrightyear{2016} \pubyear{2016}
+
+%% Some pieces required from the pandoc template
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+
+$if(tables)$
+\usepackage{longtable}
+$endif$
+
+$for(header-includes)$
+$header-includes$
+$endfor$
+
+% hyperref makes the margins screwy.
+% https://groups.google.com/forum/#!topic/latexusersgroup/4W_SwGk6zx4
+% http://ansuz.sooke.bc.ca/software/latex-tricks.php
+% \usepackage[colorlinks=true, allcolors=blue]{hyperref}
+
+\access{Advance Access Publication Date: $access_date.day$ $access_date.month$ $access_date.year$}
+\appnotes{Manuscript Category}
+
+\begin{document}
+\firstpage{1}
+
+\subtitle{$subject_section$}
+
+\title[$title_short$]{$title_full$}
+
+\author[FirstAuthorLastName \textit{et~al}.]{
+$for(author)$
+$author.name$\,\textsuperscript{$author.affiliation$},
+$endfor$
+}
+
+\address{
+$for(address)$
+\textsuperscript{$address.code$}$address.address$\\
+$endfor$
+}
+
+\corresp{$corresponding_author_text$}
+
+\history{Received on XXX; revised on XXX; accepted on XXX}
+
+\editor{Associate Editor: XXX}
+
+\abstract{
+\textbf{Motivation:} $motivation$\\
+\textbf{Results:} $results$\\
+\textbf{Availability:} $availability$\\
+\textbf{Contact:}$corresponding_author_email$\\
+\textbf{Supplementary information:} $supplementary_info$}
+
+\maketitle
+
+$body$
+
+$for(include-after)$
+$include-after$
+$endfor$
+
+% Bibliography
+\bibliographystyle{natbib}
+\bibliography{$bibliography$}
+
+\end{document}

inst/rmarkdown/templates/bioinformatics_article/skeleton/.gitignore

@@ -0,0 +1,3 @@
+*.tex
+*.pdf
+!OUP*.pdf

inst/rmarkdown/templates/bioinformatics_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}}