Package 'jss'

Coercion to Bibentry Objects

Description

Generic function and method for coercion to objects of class "bibentry".

Usage

as.bibentry(x, ...)

## S3 method for class 'jss'
as.bibentry(x, keytype = c("number", "author"), doi = TRUE, url = !doi, ...)

Arguments

x	an object (of class "jss").
keytype	character specifying which type of bib key should be generated.
doi	logical. Should the DOI be included in the bibentry?
url	logical. Should the URL be included in the bibentry?
...	arguments passed to methods.

Details

Currently only a method for objects of class "jss" is provided.

Value

An object of class "bibentry".

See Also

jss, bibentry

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Fix BibTeX Files According to JSS Style Guidelines

Description

Utilities for processing BibTeX files, adding DOIs etc., especially for publications in the Journal of Statistical Software.

Usage

fix_bib(x = NULL, file = x, orig = "_orig.bib",
  bibtool = TRUE, doi = TRUE, shortcites = TRUE, escape = TRUE)

bibtool(tex = NULL, orig = "_orig.bib")

shortcites(x, maxlength = 6)

get_doi(x, minscore = 1.5, type = NULL)
add_doi(x, file = "out.bib", minscore = 1.5)

read_bib(file, ...)

Arguments

x	character or bibentry object. If NULL the first BibTeX file in the current working directory is used. If a character is supplied it is read into a bibentry object using read.bib.
file	character for output BibTeX file name.
orig	character with file name for copy of the original BibTeX file (if any).
bibtool	logical. Should bibtool be run first (usually to remove bibentries that are not cited)?
doi	logical. Should DOIs be added using get_doi (based on cr_works)?
shortcites	logical. Should bibentries with a long author list be reported in a shortcites statement?
escape	logical or character. Should encoded text (non-ASCII, e.g., for accent and umlaut characters) be preserved in BibTeX output (FALSE) or escaped by their LaTeX representations (TRUE, default)? Instead of TRUE it is also possible to indicate the encoding of the text (e.g., escape = "UTF-8") explicitly.
tex	character specifying the input LaTeX file.
maxlength	numeric. Maximum number of authors for a normal cite (that does not have to be shortened).
minscore	numeric. Minimum score that needs to be achieved when querying a DOI.
type	character. The reference type (e.g., "journal-article" or "book") that needs to be matched.
...	further arguments passed to read.bib.

Details

The fix_bib function is a utility to automatically bring a .bib file almost into JSS style. By default, it proceeds by reading a .bib file using read.bib, omitting unused entries using bibtool, modifying author names, titles, journals, etc. if necessary, adding DOIs for articles and books using cr_works, and writing the result again to the same .bib file.

Some steps can be switched off by setting the corresponding arguments. Standalone functions for these steps are also provided.

Value

fix_bib and add_doi return an object of class "bibentry" (invisibly if an output file is specified).

bibtool returns a logical, only indicating whether the file renaming worked.

shortcites and get_doi return character vectors with BibTeX keys and DOIs, respectively.

See Also

jss

Examples

bibfile <- system.file("bib", "example.bib", package = "jss")

if(require("bibtex")) {

## read BibTeX entry as currently stored
bde1 <- read.bib(bibfile)
print(bde1)
toBibtex(bde1)

## fix BibTeX entry
## - but do not overwrite file
## - running bibtool is not necessary (and also not possible as there is no .tex file)
## - querying the DOI is switched off (just to save processing time in this example)
bde2 <- fix_bib(bibfile, file = FALSE, bibtool = FALSE, doi = FALSE)
print(bde2)
toBibtex(bde2)
## This has
## - a capitalized title,
## - correctly spaces the middle initials,
## - unifies the TAS journal name,
## - and the DOI could be added by setting doi = TRUE or manually queried via
## get_doi(bde2)

## cleanup
file.remove("_orig.bib")
}

---

Fix R Scripts to use JSS's Preferred Formatting

Description

The function fix_rscript is just a simple convenience interface to tidy_source, using certain argument settings. The code_lines function is a small utility for counting lines after removing comments and empty lines.

Usage

fix_rscript(file = NULL)

code_lines(path = ".", comment = "#")

Arguments

file	character. The .R script that should be fixed, by default Sys.glob("*.R") is used.
path	character specifying a directory with .R files.
comment	character for beginning comments.

See Also

tidy_source

---

Obtain ORCID Links for Authors

Description

Query https://orcid.org in order to obtain orcidlinks for all authors in a JSS paper.

Usage

get_orcidlink(person = NULL, rows = 1L, verbose = TRUE, ...)

Arguments

person	character, person object, or jss object. In case of a character it can either be the file name of a JSS-style LaTeX file (by default the first LaTeX file in the current working directory is used) or person names (optionally enhanced by ORCID search strings).
rows	integer. The number of search results for each author.
verbose	logical. Should results be printed to the screen and the ORCID URL opened in the browser? If set to TRUE, results are returned invisibly.
...	further arguments passed to orcid.

Details

The get_orcidlink function is a utility to automatically search possible ORCID links for each author in a JSS paper. By default it reads the first LaTeX file in the current directory (assuming it is in JSS style), extracts the author names, and then uses orcid to query https://orcid.org/ for their possible ORCIDs.

All search results should be checked carefully because the chance to obtain an erroneous ORCID result is quite high if an author does not have an ORCID.

For authentication see the rorcid package. An easy option is to run orcid_auth once and put the resulting UUID string into your .Rprofile as options(orcid_token = "...").

Value

get_orcidlink returns a character matrix with the author names, ORCID links in LaTeX format, and ORCID URLs. The matrix is returned invisible if verbose = TRUE (the default).

See Also

jss, orcid

Examples

## Not run: 
get_orcidlink("Achim Zeileis")

## End(Not run)

---

Metainformation Processing for JSS Publications

Description

Utilities for processing the metainformation of (forthcoming) publications in the Journal of Statistical Software (JSS).

Usage

jss(dir = ".")

## S3 method for class 'jss'
format(x, style = "BibTeX", ...)
## S3 method for class 'jss'
as.character(x, ...)

Arguments

dir	character specifying the directory to a JSS publication along with supplementary files (if any).
x	an object of class jss.
style	character specifying the style of string that should be generated (BibTeX, CITATION, or README).
...	arguments passed to other functions.

Details

The function jss sets up a list with information about the publication and corresponding supplementary files. The resulting object of class jss can then be formatted or coerced into different formats.

Value

jss returns an object of class "jss", i.e., a list with components as follows.

key	character vector with two possible styles of bib keys,
author	character vector with LaTeX-style formatted authors,
person	person vector of authors,
title	character with simple text title,
textitle	character with LaTeX-formatted title (including proglang, pkg, etc.),
plaintitle	character with plain LaTeX-formatted title (without proglang, pkg, etc.),
journal	character with journal/section,
year	year of publication,
month	month of publication,
volume	volume,
number	issue,
pages	number of pages,
url	JSS URL,
doi	DOI,
type	type of publication (article, code snippet, book review, or software review),
directory	character with path to all files,
package	name of package(s) associated with the publication,
rpackage	logical indicating whether the publication is associated with an R package,
readme	character with path to readme.txt file (if any),
rscript	character with path to .R script (if any).

See Also

bibentry, person

---

Generate JSS LaTeX Style Files

Description

Utility functions for generating JSS's BibTeX style file (bst), LaTeX class file (cls), or a zipped archive with both files, manual, templates, logo, and further instructions.

Usage

make_jss_bst(dir = ".")
make_jss_cls(dir = ".", pdf = FALSE)
make_jss_style(dir = ".")

Arguments

dir	character specifying the output directory.
pdf	logical. Should the PDF documentation for the .cls file be generated as well?

---

Generate Files with Metainformation for JSS Publications

Description

Write selected elements of the metainformation from jss objects into text files.

Usage

make_metainfo(x = ".", ...)
make_citation(x = ".", ...)
make_readme(x = ".", ...)
make_crossref(x = ".", ..., deposit = TRUE)
make_ojs(x = ".", ...)
make_ojs2(x = ".", ...)
make_ojs3(x = ".", ...)
make_socialmedia(x = ".", density = 300, ...)

Arguments

x	an object of class jss or a character specifying the dir to be passed to jss.
...	arguments passed to format.jss.
deposit	logical. Should the metainformation be deposited with Crossref?
density	numeric. Resolution for rendering PDF to PNG.

Details

make_citation generates a CITATION file for inclusion in R packages.

make_readme generates a README.txt file for internal use in JSS.

make_metainfo generates both files and also tries to clean up and compact the manuscript LaTeX files.

make_crossref generates a CROSSREF.xml file for registering DOIs with CrossRef. If $HOME/.crossref exists and contains two lines (with login id and password, respectively), the XML is deposited automatically via curl.

make_ojs2 and make_ojs3 generate OJS.xml files for importing a new submission into OJS version 2 and 3, respectively. make_ojs creates an agnostic OJS.txt file.

See Also

jss

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