ArXiV is a place for publishing scientific technical reports and drafts which is tightly tied to LaTeX. That is why if you generate a PDF from your RMarkdown article it will tell you, hey, this has been generated using LaTeX, I want the LaTeX source. In principle, RStudio does not admit LaTeX as a final format, only .doc, .pdf or HTML. But it is no big deal.
You only need to add this to the metadata in the RMarkdown document
output:
pdf_document:
keep_tex: true
This will generate the intermediate files that are actually used to generate the PDF. You need only go to the directory where your .Rmd file is, gather the .tex and image directory (called filename_files
) with
tar cvfz filename.tgz filename.tex filename_files
and submit it to ArXiV.