Package index • easypaper

Creating a project

The project holds the paper; everything below builds it.

create_paper(): Create a reproducible Quarto manuscript project
create_example_paper(): Create an example project: a small study, written as an easypaper paper
set_paper(): Name the paper to work on
get_paper(): Which paper is named
affiliations(): The affiliations of the manuscript, under the authors

Rendering

Documents to read, written into output/. Every render checks the project first, sets the scientific names of the references in italics, and copies the figures to PNG, JPEG and TIFF at 600 dpi.

render_docx() render_pdf() render_html() render_supplementary() render_all() preview(): Render the manuscript
export_code(): Write the analysis code as one script
export_figure_formats(): Copy every figure to JPEG and TIFF
clean_cache(): Clear the knitr cache

Submitting

What you send, built into submission/: the manuscript split for double-blind review, the supplement, the figures, and the data and code compendium.

make_preprint(): Build a preprint deposit
make_submission(): Build the folder you send to a journal

Checking

What every render verifies first, to call on its own.

check_citations() check_crossrefs() check_packages() check_title() check_data() check_renv(): Check a project before rendering it
check_species(): Which scientific names of the references go in italics
check_species_text(): Check the scientific names in the text
manuscript_stats(): A summary of the manuscript

Data and metadata

data/ is the folder that publishes. convert_data() brings originals in, in a format that will still open in twenty years; the deposit’s metadata is filled in from what the project already knows.

convert_data(): Convert or copy originals into the project's data folder
deposit_zenodo(): Reserve the DOI of the data deposit on Zenodo
sync_metadata(): Fill in what the data deposit's metadata can know by itself
edit_metadata(): Describe the data deposit by hand
sync_licenses(): Copy the authors into the licences

Journals and references

Any journal’s citation style, fetched from the official CSL repository into references/; the references of the R packages, with their names kept as written; and the scientific names of any bibliography in italics.

list_journals(): The journals a project can render for
add_journal(): Add a journal's citation style to the project
write_packages_bib(): Write the references of the R packages a manuscript uses
italicize_species(): Set the scientific names of a bibliography in italics

Co-authors in Google Docs

td_upload() td_update() td_download(): Edit a section with co-authors in Google Docs

Package

easypaper easypaper-package: easypaper: automate reproducible Quarto manuscripts ready for submission