Build the folder you send to a journal

Writes submission/<label>/: the manuscript split the way journals with double-blind review ask for – a title page, and a main text that opens with the title and names nobody – or, signed, the main text alone; the supplement as its own document, every figure of the main text on its own, named with its resolution and printed size – the supplementary figures stay inside the supplement, which is how journals take them – a cover letter – dated, with the title of the manuscript, signed by the corresponding author, and with the DOI of the data once deposit_zenodo() has reserved it; for a second journal, the text of the last letter with those brought up to date – a checklist of what is left to do by hand, and the data and code compendium, zipped, ready for Zenodo or Dryad. Everything in it is rebuilt on every call except the cover letter, which is never overwritten.

Usage

make_submission(
  journal = NULL,
  label = NULL,
  caption_style = "default",
  figure_format = "tiff",
  blind = TRUE,
  snapshot = TRUE,
  suppl_figures = "separate",
  line_numbers = TRUE,
  line_spacing = 2,
  suppl_line_spacing = 1.5,
  figure_dpi = NULL,
  path = NULL
)

Arguments

journal: The citation style, by the name of its .csl without the extension (see list_journals()). NULL, the default, takes the one the manuscript declares in its csl: line.
label: Names the folder inside submission/ and every file in it. Left alone it is the journal's own name with the spaces taken out: "ecology-letters" gives submission/EcologyLetters/. A submission is never overwritten: when the folder is already there, the next version is built beside it – JournalofEcology_v2, _v3 – with its files named the same way. Pass your own label for a trial you want to keep apart.
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".
blind: TRUE (the default) splits the manuscript for double-blind review: a title page with the authors and the sections that identify them, a main text that names nobody, and a copy of the compendium that names nobody either. FALSE sends one signed main text, with all of it, and no title page.
snapshot: TRUE (the default) records renv.lock before building the compendium. FALSE leaves a lockfile you maintain by hand alone.
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 main text and of the title page, continuously, which is what reviewers cite. FALSE leaves them unnumbered.
line_spacing: The line spacing of the main text and of the title page: 2 (the default, double), 1.5 or 1.
suppl_line_spacing: The line spacing of the supplement: 1.5 (the default), 1 or 2. Its lines are not numbered.
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 submission folder, invisibly.

Details

It records renv.lock first: the project's records the environment this submission came out of, the version of easypaper that built it included, and the compendium gets one of its own, with the packages its analysis loads and what they need, and not easypaper, which the analysis does not run.

Double-blind review also needs the sections that identify you off the main text. They move to the title page: by default the Acknowledgements, the CRediT statement, the conflict of interest statement and the data availability statement, which is the list blinded-sections: sets in the easypaper: block of _quarto.yml, in the order they come out on the title page. The page is built from the manuscript and needs no file of its own; a title_page.qmd in the project, to add a running head or a word count, is used as the page.

The compendium is signed: data_and_code.zip is the one deposited, and a deposit names its authors. A double-blind submission also gets data_and_code_blinded.zip, for the reviewers: the same compendium with the authors taken out of what the package writes into it – the creators of the metadata (creators.csv, dataspice.json and its page), the copyright line of LICENSE-CODE.txt, the README – and out of renv.lock, which records the authors of every package it lists and the pages of each, and easypaper itself, which the analysis does not use and which, installed from GitHub, names the account it came from. A name, email, ORCID, affiliation or account of an author still found in it – in a script, in the data, a package of yours installed from GitHub – is reported with the file it is in, to take out of the project by hand. An account is the user part of an author's email and the owner of the project's GitHub repository.

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_submission(path = dir)
make_submission(path = dir)
make_submission("ecology-letters", figure_format = "png", blind = FALSE,
                path = dir)
list.files(file.path(dir, "submission"))
} # }
unlink(dir, recursive = TRUE)

Usage

Arguments

Value

Details

See also

Examples