README.md

Rdpack provides functions for manipulation of R documentation objects, including function reprompt() for updating existing Rd documentation for functions, methods and classes; function rebib() for import of references from bibtex files; a macro for importing bibtex references which can be used in Rd files and roxygen2 comments; and other convenience functions for references.

Table of Contents

  1. Installing Rdpack
  2. Inserting Bibtex references
    1. Preparation
    2. Inserting references
    3. Inserting citations
    4. Development using *devtools"
  3. Using Rdpack::reprompt()
    1. What it does
    2. Reprompt and open in an editor
  4. Viewing Rd files

Installing Rdpack

The latest stable version is on CRAN.

install_packages("Rdpack")

You can also install the development version of Rdpack from Github:

library(devtools)
install_github("GeoBosh/Rdpack")

Inserting Bibtex references

The simplest way to insert Bibtex references is with the Rd macro \insertRef. Just put \insertRef{key}{package} in the documentation to insert item with key key from file REFERENCES.bib in your package package. For this to work the DESCRIPTION file of the package needs to be amended, see below the full details.

Preparation

To prepare a package for importing BibTeX references it is necessary to tell the package management tools that package Rdpack and its Rd macros are needed. The references should be put in file inst/REFERENCES.bib. These steps are enumerated below in somewhat more detail, see also the vignette Inserting_bibtex_references.

  1. Add the following lines to file "DESCRIPTION":

    Imports: Rdpack
    RdMacros: Rdpack
    

    Make sure the capitalisation of RdMacros: is as shown. If the field RdMacros: is already present, add "Rdpack" to the list on that line. Similarly for field "Imports".

  2. Add the following line to file "NAMESPACE":

    importFrom(Rdpack,reprompt)
    

    The equivalent line for roxygen2 is

    #' @importFrom Rdpack reprompt
    
  3. Create file REFERENCES.bib in subdirectory inst/ of your package and put the BibTeX references in it.

Inserting references

Once the steps outlined above are done, references can be inserted in the documentation as

\insertRef{key}{package}

where key is the bibtex key of the reference and package is your package. This works in Rd files and in roxygen documentation chunks.

Usually references are put in section references. In an Rd file this might look something like:

\references{
\insertRef{Rdpack:bibtex}{Rdpack}

\insertRef{R}{bibtex}
}

The equivalent roxygen2 documentation chunk would be:

#' @references
#' \insertRef{Rpack:bibtex}{Rdpack}
#'
#' \insertRef{R}{bibtex}

The first line above inserts the reference with key Rpack:bibtex in Rdpack's REFERENCES.bib. The second line inserts the reference labeled R in file REFERENCES.bib from package bibtex.

The example above demonstrates that references from other packages can be inserted (in this case bibtex), as well. This is strongly discouraged for released versions but is convenient during development. One relatively safe use is when the other package is also yours - this allows authors of multiple packages to not copy the same refences to each of their own packages.

For further details see the vignette Inserting_bibtex_references (development version on github) or open it from R:

vignette("Inserting_bibtex_references", package = "Rdpack")

Inserting citations

From version 0.6-1 of "Rdpack", additional Rd macros are available for citations. They can be used in both Rd and roxygen2 documentation.

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

\insertCite{parseRd,Rpack:bibtex}{Rdpack} produces (Murdoch 2010; Francois 2014) and \insertCite{Rpack:bibtex}{Rdpack} gives (Francois 2014)

By default the citations are parenthesised \insertCite{parseRd}{Rdpack} produces (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 would be produced with \insertCite{parseRd}{Rdpack} and \insertCite{parseRd;textual}{Rdpack}, respectively. This also works with several citations, e.g.

\insertCite{parseRd,Rpack:bibtex;textual}{Rdpack} produces: Murdoch (2010); Francois (2014).

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{R}{bibtex} and \insertNoCite{*}{utils} record the specified references for inclusion by \insertAllCited.

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

\insertAllCited

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

#' @references
#'     \insertAllCited

To mix the citations with other text, such as ``see also'' and ``chapter 3'', write the list of keys as a 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 @Rpack:bibtex}{Rdpack}
\insertCite{@see also @parseRd; @Rpack:bibtex}{Rdpack}
\insertCite{@see also @parseRd and @Rpack:bibtex;textual}{Rdpack}

produces:

(see also Murdoch 2010 and Francois 2014)

(see also Murdoch 2010; Francois 2014)

(see also Murdoch (2010) and Francois (2014))

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

Development using *devtools"

The described procedure works transparently in roxygen2 chunks and with Hadley Wickham's package devtools. Packages are built and installed properly with the devtools commands and the references are processed as expected.

Currently (2017-08-04) if you run help commands ?xxx for functions from the package you are working on in developement mode and their help pages contain references, you may encounter some puzzling warning messages, something like:

1: In tools::parse_Rd(path) :
  ~/mypackage/man/abcde.Rd: 67: unknown macro '\insertRef'

These warnings are harmless - the help pages are built properly and no warnings appear outside developer's mode, e.g. in a separate R~session. See below for a way to inspect help pages directly from Rd files.

If you care, here is what happens. These warnings appear because devtools reroutes the help command to process the developer's Rd sources (rather than the documentation in the installed directory) but doesn't tell parse_Rd where to look for additional macros. Indeed, the message above shows that the error is in processing a source Rd file in the development directory of the package and that the call to parse_Rd specifies only the file.

Using Rdpack::reprompt()

What it does

Rdpack::reprompt() updates Rd documentation. In the most common case when it is called on an Rd file, it updates the documentation of all functions, methods and classes documented in the file. For functions this includes updating the usage section, adding missing aliases and \item's for arguments not described yet. For methods and classes entries for new methods and slots are updated in a similar way. See the documentation for details.

Rdpack::reprompt() can also be invoked on an object or the name of an object, just as utils::prompt. In that case it checks for installed documentation for the object and works on it if found. Otherwise it creates an Rd file with initial content similar to the one generated by utils::prompt but modified so that the package can be built.

If a new function, say newfun is to be documented in an existing Rd file, just add newfun() to the usage section in the file and call Rdpack::reprompt() to insert the correct usage statement, add an alias, and add items for any new arguments.

Rdpack::reprompt() does not remove anything that has become obsolete but it alerts the user to remove aliases, methods, and descriptions of arguments that have been removed.

Reprompt and open in an editor

To open the reprompt()-ed file, argument edit can be used. For this to work, options("editor") needs to be set suitably but it usually is. If edit = TRUE, then Rdpack::reprompt() will open the Rd file in an editor. For more convenient access to this feature, use Rdpack::ereprompt() (edit reprompt), which calls Rdpack::reprompt() with edit = TRUE and sets the output filename to be the same as the input filename.

In RStudio, reprompt() can be invoked on the Rd file being edited or the selected name of an object in a source code file using RStudio add-in Repropmpt (contributed by Duncan Murdoch). Obviously, this makes sense only for Rd files not generated by roxygen2.

In Emacs/ESS there are various ways to use Rdpack::reprompt() and Rdpack::ereprompt(). If options("editor") is set to emacsclient, Rdpack::ereprompt is one option. It can also be assigned to a key (wrapped in Elisp code), for example to be invoked on the currently edited file. Such a function and example key binding can be found at georgisemacs.

Viewing Rd files

A function, viewRd() to view Rd files in the source directory of a package was introduced in version 0.4-23 of Rdpack. A typical user call would look something like:

Rdpack::viewRd("./man/filename.Rd")

By default the requested help page is shown in text format. To open the page in a browser, set argument 'type' to "html":

Rdpack::viewRd("./man/filename.Rd", type = "html")

Users of 'devtools' can use viewRd in place of help() to view rendered Rd sources. This should work also in development mode on any platform (e.g. RStudio, Emacs/ESS, Rgui).



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Rdpack documentation built on April 1, 2018, 12:15 p.m.