Insert bibtex references in Rd and roxygen2 documentation

Package Rdpack provides Rd macros for inserting references and citations from bibtex files into R documentation. Function insert_ref() is the workhorse behind this mechanism. The description given on this page should be sufficient, for more details see the vignette.

Usage

insert_ref(key, package = NULL, ..., cached_env = NULL)

Arguments

key: the bibtex key of the reference, a character string.
package: the package in which to look for the bibtex file.
...: further arguments to pass on to get_bibentries(). The only one of interest to users is bibfile, whose default is "REFERENCES.bib", see get_bibentries.
cached_env: environment, used to avoid repeatedly passing the bib file from scratch, mainly used by the Rd macros.

Details

insert_ref extracts a bibliograhic reference from a bibtex file, converts it to Rd format and returns a single string with embedded newline characters. It is the workhorse in the provided mechanism but most users do not even need to know about insert_ref.

Package Rdpack provides several Rd macros for inserting references and citations in the documentation of a package. All macros work in both, manually written Rd files and in roxygen2 documentation chunks. The macros look for references in file "REFERENCES.bib" in the root of the installation directory of the package. When a package is in development mode under devtools, "inst/REFERENCES.bib" in the development directory of the package is checked first. See also get_bibentries but note that while direct calls to insert_ref() can specify a different file, the filename and the places where it is looked for are fixed for the Rd macros.

The description below assumes that Rdpack has been added to file DESCRIPTION, as described in Rdpack-package and vignette "Inserting_bibtex_references". The Rd macros are put in the text of documentation sources (‘Rd’ files or ‘roxygen2’ chunks).

Rd macro insertRef

\insertRef{key}{package} inserts the reference with bibtex key key from file "REFERENCES.bib" in package package. Argument ‘package’ can be any installed R package, not necessarily the one of the documentation object, as long as it contains file "REFERENCES.bib" in the root of its installation directory. The references are partially processed when the package is built.

References inserted with \insertRef appear in the place where the macro is put, usually in a dedicated references section (\references in Rd files, @references in roxygen chunks).

For example, section ‘References’ of this help page shows (among other things)) the rendered results of the following lines in the Rd source file:


        \insertRef{Rpackage:rbibutils}{Rdpack}
    
        \insertRef{parseRd}{Rdpack}
        
        \insertRef{bibutils6.10}{rbibutils}

A roxygen2 documentation chunk might look like this:


        #' @references
        #' \insertRef{Rpackage:rbibutils}{Rdpack}
        #' 
        #' \insertRef{parseRd}{Rdpack}
        #' 
        #' \insertRef{bibutils6.10}{rbibutils}

The first reference has label Rpackage:rbibutils and is taken from file "REFERENCES.bib" in package Rdpack. The third reference is from the file "REFERENCES.bib" in package rbibutils.

For more details see vignette "Inserting_bibtex_references".

Rd macro insertCite

\insertCite{key}{package} cites the key and records it for use by \insertAllCited, see below. key can contain more keys separated by commas.

`\insertCite{parseRd,Rpackage:rbibutils}{Rdpack}`	(Murdoch 2010; Boshnakov and Putman 2020)	`\insertCite{Rpackage:rbibutils}{Rdpack}`
(Boshnakov and Putman 2020)	`\insertCite{bibutils6.10}{rbibutils}`	(Putnam 2020)

By default the citations are parenthesised (Murdoch 2010) . To get textual citations, like Murdoch (2010) , put the string ;textual at the end of the key. The references in the last two sentences were produced with \insertCite{parseRd}{Rdpack} and \insertCite{parseRd;textual}{Rdpack}, respectively. This also works with several citations, e.g.
\insertCite{parseRd,Rpackage:rbibutils;textual}{Rdpack} produces: Murdoch (2010); Boshnakov and Putman (2020) .

To mix the citations with other text, such as ‘see also’ and ‘chapter 3’, write the list of keys as free text, starting it with the symbol @ and prefixing each key with it. The @ symbol will not appear in the output. For example, the following code


        \insertCite{@see also @parseRd and @Rpackage:rbibutils}{Rdpack},
    
        \insertCite{@see also @parseRd; @Rpackage:rbibutils}{Rdpack},
    
        \insertCite{@see also @parseRd and @Rpackage:rbibutils;textual}{Rdpack}.

produces:

(see also Murdoch 2010 and Boshnakov and Putman 2020) ,

(see also Murdoch 2010; Boshnakov and Putman 2020) ,

see also Murdoch (2010) and Boshnakov and Putman (2020) .

In the parenthesised form, adding ;nobrackets at the end of the list of keys causes the enclosing parentheses to be dropped. This is useful if you wish to use markup for the text surrounding the references. For example,


        (\emph{see also}  \insertCite{@@parseRd; @Rpackage:rbibutils;nobrackets}{Rdpack}).

gives: (see also Murdoch 2010; Boshnakov and Putman 2020 ). Without ‘;nobrackets’ the result would be (see also (Murdoch 2010; Boshnakov and Putman 2020) ).

Rd macro insertNoCite

The macro \insertNoCite{key}{package} records one or more references for \insertAllCited but does not cite it. Setting key to * will include all references from the specified package. For example, \insertNoCite{parseRd}{Rdpack} and \insertNoCite{*}{rbibutils} record the specified references for inclusion by \insertAllCited.

Rd macro insertAllCited

\insertAllCited inserts all references cited with \insertCite and \insertNoCite. Putting this macro in the references section will keep the references up to date automatically. The Rd section may look something like:


       \references{    
         \insertAllCited{}
       }

or in roxygen2, the references chunk might look like this:


       #' @references
       #'   \insertAllCited{}

Rd macro insertNoCite

\insertCiteOnly{key}{package} is as \insertCite but does not include the key in the list of references for \insertAllCited.

Value

for insert_ref, a character string

References

For illustrative purposes there are two sets of citations below The first set of references is obtained with \insertRef for each reference:

Duncan Murdoch (2010). “Parsing Rd files.” https://developer.r-project.org/parseRd.pdf.

Georgi N. Boshnakov, Chris Putman (2020). rbibutils: Convert Between Bibliography Formats. https://CRAN.R-project.org/package=rbibutils.

Putnam C (2020). “Library bibutils, version 6.10.” https://sourceforge.net/projects/bibutils/.

----

The following references are obtained with a single \insertAllCited{}. The references are sorted automatically by the surnames of the authors:

Georgi N. Boshnakov, Chris Putman (2020). rbibutils: Convert Between Bibliography Formats. https://CRAN.R-project.org/package=rbibutils.

Duncan Murdoch (2010). “Parsing Rd files.” https://developer.r-project.org/parseRd.pdf.

Chris Putnam (2020). “Library bibutils, version 6.10.” https://sourceforge.net/projects/bibutils/.

Author

Georgi N. Boshnakov

Examples

cat(insert_ref("Rpackage:rbibutils", "Rdpack"), "\n")
#> Georgi
#> N. Boshnakov, Chris Putman (2020).
#> \emph{rbibutils: Convert Between Bibliography Formats}.
#> \url{https://CRAN.R-project.org/package=rbibutils}.