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.