Add PLOS One version of the paper

README.Rmd

@@ -29,6 +29,10 @@ Please cite this package as:
 
 Chan CH, Schoch D (2023) rang: Reconstructing reproducible R computational environments. arXiv preprint:[2303.04758](https://doi.org/10.48550/arXiv.2303.04758)
 
+Please cite this package as:
+
+Chan CH, Schoch D (2023) rang: Reconstructing reproducible R computational environments. arXiv preprint:[2303.04758](https://doi.org/10.48550/arXiv.2303.04758)
+
 ## Installation
 
 You can install the development version of rang like so:

paper/Makefile

@@ -1,4 +1,27 @@
-render: bib
+render:
+	bash clean.sh ## clean up the plos theme
 	quarto render paper.qmd
 bib:
 	bibcon -b ~/dev/dotfiles/bib.bib -o paper.bib paper.qmd
+diff: render
+	cp paper_r0.tex temp1.tex
+	-latex temp1
+	-bibtex temp1
+	pdflatex temp1
+	pdflatex temp1
+	perl latexpand --expand-bbl temp1.bbl temp1.tex > flat1.tex
+	cp paper.tex temp2.tex
+	-latex temp2
+	-bibtex temp2
+	pdflatex temp2
+	pdflatex temp2
+	perl latexpand --expand-bbl temp2.bbl temp2.tex > flat2.tex
+	cp flat2.tex paper_flat.tex
+	latexdiff flat1.tex flat2.tex > diff.tex
+	-pdflatex diff.tex
+	-pdflatex diff.tex
+	rm temp*
+	rm flat*
+	rm diff.aux
+	rm diff.log
+	rm diff.tex

paper/before-body.tex

@@ -0,0 +1,39 @@
+$-- PLOS insert title and author within the main body
+$-- Use this template to insert the necessary pieces before any content provided in .qmd file
+\vspace*{0.2in}
+
+% Title must be 250 characters or less.
+\begin{flushleft}
+{\Large
+\textbf\newline{$title$} % Please use "sentence case" for title and headings (capitalize only the first word in a title (or heading), the first word in a subtitle (or subheading), and any proper nouns).
+}
+\newline
+\\
+% Insert author names, affiliations and corresponding author email (do not include titles, positions, or degrees).
+$by-author:_authors.tex()[, ]$
+\\
+\bigskip
+$by-affiliation:_affiliations.tex()[\\ ]$
+\bigskip
+
+
+% Use the asterisk to denote corresponding authorship and provide email address in note below.
+$for(by-author)$
+$if(by-author.attributes.corresponding)$
+* $by-author.email$
+$endif$
+$endfor$
+
+\end{flushleft}
+
+$if(abstract)$
+\section*{Abstract}
+$abstract$
+$endif$
+
+$if(author-summary)$
+\section*{Author summary}
+$author-summary$
+$endif$
+
+\linenumbers

paper/clean.sh

@@ -0,0 +1,5 @@
+if grep -q "\\Yinyang" _extensions/quarto-journals/plos/partials/before-body.tex ;
+then
+   cp before-body.tex _extensions/quarto-journals/plos/partials/before-body.tex
+fi
+