Package 'rjtools'

Create an R Journal article with the existing template

Description

Create an R Journal article with the existing template

Usage

create_article(
  name = "test",
  file = xfun::with_ext(name, "Rmd"),
  create_dir = FALSE,
  edit = TRUE
)

Arguments

name	the name of the Rmd, will default to "test"
file	File name for the draft
create_dir	TRUE to create a new directory for the document (the "default" setting leaves this behavior up to the creator of the template).
edit	TRUE to edit the template immediately

Details

Outputs an R Journal paper template set of files in the directory specified by dir_path or in the project directory, if nothing is specified. See vignette("create_article", package = "rjtools") for more details on how to create and format an article.

---

A single article check

Description

A single article check

Usage

initial_check_article(
  path,
  dic = "en_US",
  pkg,
  ...,
  ask = interactive(),
  logfile = file.path(path, "initial_checks.log")
)

check_filenames(path)

check_structure(path)

check_folder_structure(path)

check_unnecessary_files(path)

check_cover_letter(path)

check_title(path, ignore = "")

check_section(path)

check_abstract(path)

check_spelling(path, dic = "en_US", ...)

check_proposed_pkg(pkg, ask = interactive())

check_pkg_label(path)

check_packages_available(path, ignore)

check_bib_doi(path)

check_csl(path)

check_date(path, file)

get_orcid(path, file = NULL)

Arguments

path	string, path to the directory that contains the .tex file (Ideally, this directory should contain .bib, .Rmd, and .tex with author names and two RJwrapper files: RJwrapper.pdf and RJwrapper.tex)
dic	string, the dictionary used for spelling check. See dict argument in hunspell::hunspell()
pkg	string, optional. The name of the proposed package (if relevant), to be checked for activity on CRAN
...	additional arguments for spelling check with hunspell::hunspell
ask	logical, if TRUE then checks may ask the user for interactive input of missing information.
logfile	a connection for the output log, or a string with the filename of the output log or NULL if no log should be written
ignore	The words to ignore in title check, use c(pkg, pkg, ...) for multiple quoted words
file	string, the file name if multiple files are detected under the path argument

Details

Folder structure checks:

• check_filenames(): the three files (.bib, .Rmd, and .tex) all present and have consistent names

• check_structure(): check validity of all filenames and depth of the directory structure

• check_unnecessary_files(): the template file (i.e., RJtemplate.tex) is not included in the directory

• check_cover_letter(): a motivational letter

Content checks:

• check_title(): article title is in title case

• check_section(): section sections are in sentence case

• check_abstract(): abstract should be plain text without package markups (CRANpkg, BIOpkg, pkg), math notations($...$), citations, and other formattings (highlight, italic, etc)

• check_spelling(): potential spelling mistakes

• check_proposed_pkg(): package proposed in the paper is on CRAN

• check_pkg_label(): packages marked up with are not available on CRAN or BioConductor

• check_packages_available(): packages mentioned in the article are available on CRAN

• check_bib_doi: whether bib entries have DOI or URL included, uncless can't sourced online

• check_csl: no additional csl file should be used consistent, either in sentence (preferred) or title case

See vignette("create_article", package = "rjtools") for how to use the check functions

Value

list of all results (see log_error for details). You can use unlist() to get a character vector of the result statuses.

Examples

your_article_path <- system.file("sample-article", package = "rjtools")
if (interactive()) initial_check_article(your_article_path)

---

Keywords options for R Journal

Description

Available keywords options for R Journal articles

Usage

keywords

Format

A vector of length 41

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Prepare pre-filled fields in the submission form prep_submission generate some answers based on the .tex file to fill the article submission form. You can save the answers if assigned it to an object.

Description

Prepare pre-filled fields in the submission form prep_submission generate some answers based on the .tex file to fill the article submission form. You can save the answers if assigned it to an object.

Usage

prep_submission()

Value

a list

---

R Markdown output formats for R Journal articles

Description

The R Journal is built upon the distill framework with some modifications. This output format behaves almost identically to the distill::distill_article() format, with some formatting and structural changes. The rjournal_article() format will produce both HTML and PDF outputs, while the rjournal_pdf_article() produces only the PDF output.

Usage

rjournal_article(toc = FALSE, self_contained = FALSE, legacy_pdf = FALSE, ...)

rjournal_pdf_article(..., self_contained = FALSE)

rjournal_web_article(toc = FALSE, self_contained = FALSE, ...)

Arguments

toc	TRUE to include a table of contents in the output
self_contained	Produce a standalone HTML file with no external dependencies, using data: URIs to incorporate the contents of linked scripts, stylesheets, images, and videos. Note that even for self contained documents MathJax is still loaded externally (this is necessary because of its size).
legacy_pdf	whether an article is from the past and only have pdf version
...	Arguments passed to distill::distill_article() for web articles, and rticles::rjournal_article() for pdf articles.

Value

the rendered R Journal article

---

R Markdown output formats for R Journal issues

Description

The R Journal is built upon the distill framework with some modifications. This output format produces the PDF for an R Journal issue.

The R Journal is built upon the distill framework with some modifications. This output format behaves almost identically to the distill::distill_article() format, with some formatting and structural changes.

Usage

rjournal_pdf_issue(..., render_all = FALSE)

rjournal_web_issue(toc = FALSE, self_contained = FALSE, rnews = FALSE, ...)

Arguments

...	Arguments passed to distill::distill_article().
render_all	Re-render all articles in the issue, even if the page numbers have not changed.
toc	TRUE to include a table of contents in the output
self_contained	Produce a standalone HTML file with no external dependencies, using data: URIs to incorporate the contents of linked scripts, stylesheets, images, and videos. Note that even for self contained documents MathJax is still loaded externally (this is necessary because of its size).
rnews	This issue is from R News.

Value

an generated R Journal issue

---

Submit a paper to the R Journal

Description

This is a final self-check function, similar to that runs through a checklist on your submission that cannot be done automatically.

Usage

submit_rjournal()

---

Zip your directory for R Journal submission

Description

zip_paper will first check the folder structure with check_folder_structure() before zipping up everything in the main directory, excluding the .Rproj file, if exist.

Usage

zip_paper()

Value

a zip file for an R Journal submission

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