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Build a preprint deposit

Source: R/submission.R
make_preprint.Rd

make_submission()'s sibling, for the other destination. Writes submission/<label>/: the manuscript as ONE signed PDF – a preprint carries its authors, and is not reviewed blind – its supplement as PDF too, every figure on its own, and the data and code compendium, zipped. There is no cover letter: there is no editor. Nor is there a short title, even when the manuscript has one: a running head is what a journal asks for, not a preprint server. The supplement names the server where a journal's would name the journal – "Preprint, bioRxiv" – since the paper is in no journal yet. A README.md inside says what goes to the preprint server and what goes to the data repository, and what to do before pressing submit.

Usage

make_preprint(
  journal = NULL,
  label = "bioRxiv",
  caption_style = "default",
  figure_format = "tiff",
  snapshot = TRUE,
  suppl_figures = "separate",
  line_numbers = TRUE,
  line_spacing = NULL,
  suppl_line_spacing = NULL,
  figure_dpi = NULL,
  path = NULL
)

Arguments

journal

The citation style. A preprint has no house style, so this is only about which convention you prefer to read. NULL takes the manuscript's own.

label

Names the folder inside submission/ and every file in it. Defaults to the server you are most likely to post to; change it for another one. Never overwritten: a second call builds the next version beside it, bioRxiv_v2, with its files named the same way.

caption_style

How figures and tables are named: "default", "abbrev", "colon", "compact", "nature", or one of your own (see render_docx()).

figure_format

The format of the standalone figures: "tiff" (what journals ask for), "png" or "jpg".

snapshot

TRUE (the default) records renv.lock before building the compendium.

suppl_figures

"separate" (the default) leaves the supplementary figures and tables in the supplement, and rewrites their citations in the main text to "Figure S1". "main" keeps them at the end of the main text. Supplementary text (an extended Methods) always goes out on its own, with its own reference list.

line_numbers

TRUE (the default) numbers every line of the manuscript PDF, continuously, which is what readers and reviewers of a preprint cite; FALSE leaves them unnumbered.

line_spacing, suppl_line_spacing

The line spacing of the manuscript and of the supplement: 1, 1.5 or 2. NULL, the default, keeps the linestretch of the pdf format in _quarto.yml – 1.5 in the template.

figure_dpi

The resolution the figures are drawn at, in dpi, for this call: NULL (the default) keeps the dpi of the knitr block of _quarto.yml, 600 in a new project. The standalone figures are named with it and with the size they print at: Figure_1_600dpi_180x120mm.tiff.

path

The project, or any folder inside it. Left out, the one set_paper() named; with none named, this stops before writing: it writes into the project, and easypaper never takes the working directory for it.

Value

The path of the deposit, invisibly.

Details

It needs a LaTeX installation for the PDF: tinytex::install_tinytex() is enough.

See also

make_submission().

Examples

dir <- file.path(tempdir(), "my_paper")
create_paper(dir, title = "Ant colonies", authors = "Ada Lovelace",
             git = FALSE)
#> Project created: /tmp/Rtmp92gqjt/my_paper
#>   1. open my_paper.Rproj
#>   2. library(easypaper)
#>   3. set_paper(".")      # the project to work on, once a session
#>   4. render_html()      # see ?render for every command

# It renders the manuscript, so it needs Quarto (https://quarto.org).
if (FALSE) { # \dontrun{
make_preprint(path = dir)
make_preprint(label = "EcoEvoRxiv", path = dir)
list.files(file.path(dir, "submission"))
} # }
unlink(dir, recursive = TRUE)