Help for package rjtools

Title:

Preparing, Checking, and Submitting Articles to the 'R Journal'

Version:

1.0.18

Description:

Create an 'R Journal' 'Rmarkdown' template article, that will generate html and pdf versions of your paper. Check that the paper folder has all the required components needed for submission. Examples of 'R Journal' publications can be found at https://journal.r-project.org.

License:

MIT + file LICENSE

Encoding:

UTF-8

RoxygenNote:

7.3.2

Imports:

distill, stringr, purrr, hunspell, fs, cli, glue, whisker, xfun, callr, rlang, yaml, yesno, utils, tinytex, bookdown, BiocManager, here, rmarkdown

Suggests:

knitr, pdftools, rstudioapi, testthat (≥ 3.0.0)

VignetteBuilder:

knitr

URL:

https://github.com/rjournal/rjtools

BugReports:

https://github.com/rjournal/rjtools/issues

Config/testthat/edition:

Depends:

R (≥ 4.1.0)

LazyData:

true

NeedsCompilation:

Packaged:

2025-01-23 21:55:37 UTC; cookd

Author:

Mitchell O'Hara-Wild [aut], Stephanie Kobakian [aut], H. Sherry Zhang [aut], Di Cook

[aut, cre], Simon Urbanek [aut], Christophe Dervieux

[aut]

Maintainer:

Di Cook <dicook@monash.edu>

Repository:

CRAN

Date/Publication:

2025-01-23 22:30:02 UTC

rjtools: Preparing, Checking, and Submitting Articles to the 'R Journal'

Description

Author(s)

Maintainer: Di Cook dicook@monash.edu (ORCID)

Authors:

Mitchell O'Hara-Wild mail@mitchelloharawild.com
Stephanie Kobakian
H. Sherry Zhang huizezhangsh@gmail.com
Simon Urbanek simon.urbanek@R-project.org
Christophe Dervieux cderv@rstudio.com (ORCID)

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

Logging functions

Description

log_... functions produce a log entry.

journal_summary prints a quick summary (status counts) based on the journal.

simplify_journal returns a simplified form of the results in the journal.

Usage

log_error(
  text,
  ...,
  output = getOption("check.log.output", "cli"),
  file = getOption("check.log.file", NULL),
  signal = getOption("check.log.conditions", FALSE),
  .envir = parent.frame()
)

log_success(
  text,
  ...,
  output = getOption("check.log.output", "cli"),
  file = getOption("check.log.file", NULL),
  signal = getOption("check.log.conditions", FALSE),
  .envir = parent.frame()
)

log_note(
  text,
  ...,
  output = getOption("check.log.output", "cli"),
  file = getOption("check.log.file", NULL),
  signal = getOption("check.log.conditions", FALSE),
  .envir = parent.frame()
)

log_warning(
  text,
  ...,
  output = getOption("check.log.output", "cli"),
  file = getOption("check.log.file", NULL),
  signal = getOption("check.log.conditions", FALSE),
  .envir = parent.frame()
)

journal_summary(journal = getOption("check.log.journal"), file = stdout())

simplify_journal(journal = getOption("check.log.journal"))

Arguments

text

string, description of the error that occurred, will be passed to glue.

...

additional inputs for text passed to the glue function.

output

type of the output, can either a string ("cli" to use the cli package (default), "R" for standard R facilities or "none" for no output) or a connection. It uses the "check.log.output" option if set.

file

connection to log a copy of the output to or NULL (default) if no additional copy is desired. It uses the "check.log.file" option.

signal

logical, if TRUE then a condition is signalled at the end of the function. All conditions have superclass "RJcheckCondition" and subclass "RJCheck<result>" where <result> is one of SUCCESS, NOTE, WARNING and ERROR. They also have the corresponding standard R condition classes. Uses option "check.log.conditions".

.envir

the environment used to find the text string replacements

journal

environment of the journal

Details

Most arguments are intended to be set with options to allow the use of the checking mechanism both in interactive and automated settings. There are four types of log entries: SUCCESS, NOTE, WARNING and ERROR. If the "check.log.journal" option is set to an environment then the entry is also added to the journal.

Value

log_... string with the result type. The corresponding condition object with a message and call is included in the "info" attribute (even if no condition is signalled).

journal_summary table of the status counts

simplify_journal string matrix with columns "result" (status), "test" (name of the calling function) and "message"

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, ...)

rjournal_pdf_article(..., self_contained = FALSE, citation_package = "natbib")

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).

...

Arguments passed to distill::distill_article() for web articles, and rticles::rjournal_article() for pdf articles.

citation_package

The LaTeX package to process citations, natbib or biblatex. Use default if neither package is to be used, which means citations will be processed via the command pandoc-citeproc.

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.

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

rnews

This issue is from R News.

Value

an generated R Journal issue

R Markdown site generator for the R Journal

Description

R Markdown site generator for Distill websites

Usage

rjournal_website(input, ...)

Arguments

input

Website directory (or the name of a file within the directory).

...

Currently unused.

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()

Various handy symbols to use in a command line UI

Description

Show symbols in console output

Usage

symbol_utf8

Format

An object of class list of length 4.

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

rjtools: Preparing, Checking, and Submitting Articles to the 'R Journal'

Description

Author(s)

See Also

Create an R Journal article with the existing template

Description

Usage

Arguments

Details

A single article check

Description

Usage

Arguments

Details

Value

Examples

Keywords options for R Journal

Description

Usage

Format

Logging functions

Description

Usage

Arguments

Details

Value

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

Usage

Value

R Markdown output formats for R Journal articles

Description

Usage

Arguments

Value

R Markdown output formats for R Journal issues

Description

Usage

Arguments

Value

R Markdown site generator for the R Journal

Description

Usage

Arguments

Submit a paper to the R Journal

Description

Usage

Various handy symbols to use in a command line UI

Description

Usage

Format

Zip your directory for R Journal submission

Description

Usage

Value

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.