First release.
create_paper() writes a Quarto project for one manuscript: the text in
_sections/, one file per section, the references and the journal's
citation style in references/, the setup of the analysis in R/setup.R
and the data in data/. The build logic lives in the package, so a fix
reaches every project with update.packages(). Also in RStudio, under
File > New Project.create_example_paper() writes the same project with a small study in it
-- the trees of Barro Colorado Island -- to see how each part is written.manuscript.qmd, the
way Quarto documents them; every render numbers the affiliations and prints
the authors on one line, as a paper does (affiliations()).easypaper: block of _quarto.yml, so they travel with
the paper.set_paper("."), or in a call with path. One that writes never takes the
working directory for the project: with none named, it stops before
writing. One that only reads takes the working directory's project when
none is named.README.md, what a repository shows first, carries the title,
the authors with their affiliations and ORCID, the keywords and the licence
notice from the first commit, and the DOI of the data once it is reserved;
every render keeps them in step with manuscript.qmd.convert_data() brings originals into data/ in open formats: workbooks
and statistical files become .csv, files already open are copied, and the
originals are only ever read. Outside a project, to says where the
results go.sync_metadata() describes the data deposit from what the project already
knows -- the title, the keywords, the authors with their affiliations,
the email of the corresponding author and their ORCID, the licence of the
data from the project's LICENSE, every file of data/, and the
variables of each table, read with its own separator (,, ; or a tab)
-- and edit_metadata() opens an editor for the rest. make_preprint() and
make_submission() compile it into dataspice.json and its page before
they build the compendium, so the deposit describes the data as they are.render_html(), render_docx(), render_pdf() and
render_supplementary() write documents to read into output/, in the
style of the journal the manuscript names or of any other; render_all()
runs render_docx(), render_pdf() and export_code() in one go.
preview() reloads as you save. Every document is named after the
project, manuscript_<project>.docx, with the journal added when it is
not the manuscript's own..docx and in the .pdf.
The affiliations and the keywords line start without the first-line
indent of the text.-@sfig-x cites the number
alone, S1. It opens with "Supporting Information" and, under it, the
reference of the paper, flush left; a preprint's names the server instead
of a journal. One that cites nothing has no reference list.dpi of
_quarto.yml (600 in a new project)..pdf sets the title block flush left, with an ORCID icon beside each
author who has one, justifies the captions, and prints the Greek letters
of the text, which LaTeX's font lacks.export_code() writes the code of every chunk into one script,
analysis_code.R, that opens with a table of contents: the line each
section starts on and the chunks it holds. Each analysis lives in the
results section that reports it, so each is found under its own heading.crossref: block of _quarto.yml, or a caption style
for one render: "abbrev", "colon", "compact", "nature", or one of
your own. The text may cite with another word than the caption's: Figure
1. under the figure, Fig. 1 in the text.list_journals() and add_journal() manage the citation styles, fetched
from the official CSL repository.write_packages_bib() writes the references of the R packages the
manuscript uses, as knitr::write_bib() does, with the names in their
titles kept as written: vegan: Community ecology package, not Vegan,
in a journal that sets titles in sentence case.?checks), and records the environment it came out of in
renv.lock; check_renv() says whether that record matches the library.italicize_species() does it for any bibliography,
into the CSL-JSON file you name, and check_species() lists the names left
in doubt.check_species_text() reads the text the way an editor does: italics,
first mention, abbreviation, authority.manuscript_stats() gives what a submission form asks for: characters of
the title, words of the abstract and the main text, references, figures
and tables. Every render prints it.make_submission() builds the folder for a journal into submission/:
double-blind by default, with a title page and a main text that names
nobody, standalone figures renumbered and named with their resolution and
printed size (Figure_1_600dpi_180x120mm.tiff; figure_dpi changes the
resolution for one call), a cover letter already dated,
titled and signed by the corresponding author -- written from the last
one, with those brought up to date, when the paper goes to a second
journal -- a checklist, and a
data and code compendium -- with a copy for the reviewers that names nobody
either. blind = FALSE for a signed manuscript.make_preprint() builds the preprint: one signed PDF and its supplement,
with the same compendium.make_submission() or
make_preprint() to the same journal or server builds the next version
beside the first, JournalofEcology_v2, with its files named the same
way.deposit_zenodo() reserves the DOI of the data on Zenodo and writes it
into the text and the cover letters, without publishing. The deposit
carries the licence of the project's LICENSE, as the data's metadata do;
an ORCID iD Zenodo could not read is left out of it, with a warning.td_upload(), td_download() and td_update() share a section with
co-authors in Google Docs, through trackdown.