Render the manuscript

Each render runs the checks first (checks), keeps the licences and the deposit's metadata in step with the manuscript, sets the scientific names of the references in italics, renders with Quarto, repairs what Word would refuse to open, and copies every figure to figures/ as PNG, JPEG and TIFF at the dpi of _quarto.yml, 600 in a new project. What it writes goes to the project's output/ folder.

Usage

render_docx(
  journal = NULL,
  caption_style = "default",
  suppl_figures = "separate",
  path = NULL
)

render_pdf(
  journal = NULL,
  caption_style = "default",
  suppl_figures = "separate",
  path = NULL
)

render_html(journal = NULL, caption_style = "default", path = NULL)

render_supplementary(
  journal = NULL,
  caption_style = "default",
  output_format = "docx",
  files = NULL,
  blind = FALSE,
  path = NULL
)

render_all(journal = NULL, caption_style = "default", path = NULL)

preview(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. Naming one here overrides that for this call only, and changes no file.
caption_style: How figures and tables are named, in their captions and where the text cites them: "default" is what the crossref: block of _quarto.yml says (Figure 1. and Table 1. in a new project). The others are "abbrev" (Fig. 1.), "colon" (Figure 1:), "compact" (Fig. 1:) and "nature" (Figure 1 |), or one you define, under a name of your choosing, in caption-styles: of the easypaper: block of _quarto.yml. The text cites with the caption's word unless the style gives it one of its own – fig-prefix beside fig-title in crossref:, or fig-text in a caption style – "Figure 1." under the figure, "Fig. 1" in the text. It does not follow journal: a citation style says nothing about figures or tables.
suppl_figures: "separate" (the default) leaves the supplementary figures and tables in the supplement, and rewrites their citations in the main text: @sfig-map becomes "Figure S1", and -@sfig-map, the number alone, "S1". "main" keeps them at the end of the manuscript instead.
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.
output_format: "docx", "pdf" or "html".
files: The supplementary sections to render. NULL, the default, renders every supplementary section: the numbered files of _sections/ with suppl in their name, 12.1_suppl_material.qmd in the template.
blind: TRUE leaves the authors off the supplement, for one that travels with a double-blind submission.

Value

The path of the file written, invisibly: several for render_supplementary() when there are several supplements. render_all() returns the output/ folder, and preview() nothing useful.

Details

Every document is named after the project, the folder its .Rproj is in: manuscript_<project>, supporting_information_<project>. Rendered in the style of a journal other than the manuscript's own, the journal is added – manuscript_<project>_ecology-letters.docx – so it leaves yours as it was. Rename the folder and the next render follows.

render_docx() writes output/manuscript_<project>.docx, on the project's Word template, and the supplement beside it, as render_supplementary() does.
render_pdf() writes output/manuscript_<project>.pdf, its lines numbered as in the .docx, and the supplement beside it as .pdf: the title block flush left, with an ORCID icon beside each author who has one, the captions justified, and the Greek letters of the text printed, which LaTeX's font lacks. It needs a LaTeX installation: tinytex::install_tinytex() is enough.
render_html() writes output/manuscript_<project>.html: the working copy, in seconds instead of minutes. It does not record renv.lock, so rendering an old version to look into something never rewrites your record.
render_supplementary() writes the supplement on its own: output/supporting_information_<project>.docx, or one file per supplementary section when there are several (_sections/12.1_suppl_*.qmd, 12.2_suppl_*.qmd ...). Its own numbering (Figure S1...), its own Word template and its own reference list, left out when it cites nothing. It opens with "Supporting Information" and, under it, the reference of the paper it belongs to.
render_all() runs render_docx(), render_pdf() and export_code(), in that order: every document to read, the supplements included, into output/. It does not build a submission: that is make_submission().
preview() opens a live preview in the browser, rendered again every time you save a .qmd.

The manuscript and its supplement always come out as separate documents, each with its own reference list. That is what a journal asks for, and the only way the tables survive: merging them means handing both to pandoc, which rebuilds the document and loses every column width.

The Word templates ship with the package. To use your own, put a file of the same name – word_plain_paper_style.docx for the manuscript, word_plain_paper_style_supplementary_material.docx for the supplement, word_cover_letter.docx for the letter – in a format/ folder in the project; it is used instead.

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

# The renders need Quarto, a program of its own (https://quarto.org).
if (FALSE) { # \dontrun{
render_html(path = dir)
render_docx(path = dir)
render_docx("ecology-letters", "abbrev", path = dir)
render_pdf(path = dir)
render_supplementary(path = dir)
render_all(path = dir)
list.files(file.path(dir, "output"))
} # }
unlink(dir, recursive = TRUE)

Usage

Arguments

Value

Details

See also

Examples