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proofreading-checklist.tex
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proofreading-checklist.tex
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\documentclass[11pt]{article}
\usepackage{a4wide}
\usepackage{hyperref}
\begin{document}
\title{R Journal Proof-reading Check List}
\author{by the R Journal Editors}
\date{11 May 2017}
\maketitle
Your article has been accepted for publication in The R Journal. To
assist the editorial board with the production of your article, please
ensure that it conforms to the following check-list and send a revised
version to the handling editor.
\subsection*{Title, authors, abstract, sections}
\begin{itemize}
\item The article title should be title case (i.e.\ all words capitalized
except for articles, conjunctions and prepositions).
\item The author list should start with ``by''.
\item The abstract should be created using the \verb+\abstract{}+
environment provided by the R Journal style file \texttt{RJournal.sty}; it
may contain references but should not contain mathematical markup;
it should always be followed by a section title.
\item Section and subsection titles should be in sentence case (i.e.\ only
the first word and proper names capitalized)
\item Use the \verb+\section+ and \verb+\subsection+ commands for sections and
subsections, not the starred versions (\verb+\section*+
and \verb+\section*+). The result may look the same but your
sections will not be properly indexed in the PDF file if you use
the starred versions.
\item All authors must have an affiliation at the end of the article,
with the email address of at least the first author; the affiliation
blocks may contain per-author ORCiD iD strings.
\end{itemize}
\subsection*{Software markup and citation}
\begin{itemize}
\item R itself should not have a citation or bibliography entry.
\item All other software (including R packages) must have a citation after
the first mention in the body text (not the abstract) and a
corresponding entry in the bibliography.
\item The first mention of a CRAN package in the body text (not the title or
abstract) should be marked up with \verb+\CRANpkg+. This
provides a hyper-link to the package homepage on CRAN. Similarly,
the first mention of a Bioconductor package should be marked up with
\verb+\BIOpkg+. It is also reasonable to cite most such packages in the
bibliography, for example produced using
\verb+toBibtex(citation("pkg", auto=TRUE))+; works in
\verb+toBibtex(citation("pkg"))+ may be added.
\item Other than the above, names of R packages should be marked up with
\verb+\pkg+, including in the title (This ensures that the
package name is correctly formatted in the table of contents).
\item It is reasonable to associate relevant text with CRAN Task Views using
the \verb+\ctv+ markup.
\item Programming languages (including R), and other sofware
(e.g. Stata, Matlab) do not have special markup but appear in the
same font as the rest of the body text.
\end{itemize}
\section*{R code}
\begin{itemize}
\item Use the \verb|example| environment for code examples.
\item Use \verb+\code{}+ to mark up functions, objects, argument names etc.\
appearing in the text. Class names should appear in double quotes.
\item Ensure that code listings do not overflow the right hand margin.
\item Use indentation and spacing to improve the readability of code
listings where possible, e.g. put spaces after commas and around
equals signs.
\end{itemize}
\section*{General LaTeX issues}
\begin{itemize}
\item As much as reasonably possible, avoid the use of extra LaTeX packages,
as these complicate the production of the journal, especially where different
articles make different choices purely for appearance.
\item Put a trailing backslash -- \verb+.\+ -- after periods followed
by a space that are not at the end of a sentence (when using e.g.,
i.e., etc.).
\item Use \verb+\url+ for all URLs. The file \texttt{RJwrapper.tex}
loads the LaTeX package ``url'' for you.
\item Use booktabs format for tables (e.g.\ \verb+\toprule+,
\verb+\midrule+, \verb+bottomrule+ rather than \verb+\hline+).
The file \texttt{RJwrapper.tex} loads the LaTeX package ``booktabs''
for you.
\item Avoid superfluous LaTeX formatting, e.g.
\begin{itemize}
\item Bold in figure captions,
\item Use of \verb+\setlength{itemsep}+ to change vertical spacing
\end{itemize}
\item Use the subcaption package for subfigures, not subfigure nor
subfig.
\end{itemize}
\section*{Mathematics}
\begin{itemize}
\item Punctuation after equations must be consistent (i.e.\ you may
use it in all equations, or not at all).
\item Formatting tools provided by the American Mathematical Society
are preferred to the default LaTeX formatting. The
\texttt{RJwrapper.tex} file loads the LaTeX packages ``amsmath'' and
``amssymb'' for you. In particular,
\begin{itemize}
\item Use \verb+pmatrix+ for matrices, not \verb+array+
\item Use \verb+align+ or \verb+alignat+ for stacked equations,
not \verb+eqnarray+.
\item If at all possible, stick to symbols from ``amssymb'' and
avoid alternative symbol fonts.
\end{itemize}
\item In displayed formulae, use \verb+\left(+ and \verb+\right+, not
\verb+(+ and \verb+)+ to ensure correct sizing of braces.
\item Do not leave empty lines before displayed formulae, and only
leave a blank line after a displayed formula if there is a paragraph
break.
\item Use \verb+$-5$+ not \verb+-5+ for a true minus prefix.
\end{itemize}
\section*{Bibliography}
\begin{itemize}
\item The bibliography should be created with BibTeX, and the BibTeX
sources included in the submission.
\item Bibliography entries should contain DOI where available, following: \url{https://www.crossref.org/display-guidelines/}, formatted
as \verb+url = {https://doi.org/<doi>}+.
\item False given DOI formatted as above for article entries can be checked, and attempts to find unknown DOI values for article entries can be made using the \verb+check_doi()+ and \verb+find_doi()+ functions in the \verb+doi_helpers.R+ file at \url{https://journal.r-project.org/share/doi\_helpers.R}
\item Do not use url fields to link to publishers if a DOI is available; all links for entries with DOIs must be through the DOI key.
\item Bibliography entries should not contain any markup specific to
The R Journal. For example, package names should not be marked up
with \verb+\pkg+ in the bibliography.
\item Acronyms and proper names in titles should be protected with
braces \verb+{}+ to ensure that they appear properly capitalized
in the bibliography. Likewise, corporate authors should be
protected to ensure that they appear verbatim and are not abbreviated.
\item Do not override the default bibliography style.
\end{itemize}
\end{document}