Update and Manipulate Rd Documentation Objects

Functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating 'Rd' documentation for functions, methods and classes; 'Rd' macros for citations and import of references from 'bibtex' files for use in 'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and inserting snippets of 'R' code and the results of its evaluation or creating graphics on the fly; and many functions for manipulation of references and Rd files.

Rdpack provides functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating existing Rd documentation for functions, methods and classes; Rd macros for citations and import of references from bibtex files for use in Rd files and roxygen2 comments (\insertRef, \insertCite, \insertAllCited); Rd macros for evaluating and inserting snippets of R code and the results of its evaluation (\printExample) or creating graphics on the fly (\insertFig); and many functions for manipulation of references and Rd files.

1. Installing Rdpack
2. Inserting Bibtex references and citations
   1. Preparation
   2. Inserting references
   3. Inserting citations
   4. Changing the style of references
   5. Troubleshooting
      1. A puzzling message in devtools development mode
      2. Typical errors
   6. Latex markup in BibTeX entries
   7. Encoding of file REFERENCES.bib
3. Viewing Rd files
4. Using Rdpack::reprompt()
   1. What it does
   2. Reprompt and open in an editor
5. Inserting evaluated examples
   1. Evaluating the examples in section Examples
6. Inserting figures/graphs/plots
7. Versions of Rdpack

Installing Rdpack

Install the latest stable version from CRAN:

install_packages("Rdpack")

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

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

Inserting Bibtex references and citations

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. Alternatively, use one or more \insertCite{key}{package} commands to cite works from REFERENCES.bib, then issue a single \insertAllCited{} directive to produce a list of all cited references. 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 or open it from R:

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

(The latest version of the vignette is at Inserting_bibtex_references (development version on github).)

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.

Changing the style of references

Bibliography styles for lists of references are supported from Rdpack (>= 0.8). Currently the only alternative offered is to use long names (Georgi N. Boshnakov) in place of the default style (Boshnakov GN). More comprehensive alternatives can be included if needed or requested.

To cause all lists of references produced by \insertAllCited in a package to appear with full names, add .onLoad() function to your package. If you don't have .onLoad(), just copy the following definition:

.onLoad <- function(lib, pkg){
    Rdpack::Rdpack_bibstyles(package = pkg, authors = "LongNames")
    invisible(NULL)
}

If you already have .onLoad(), add the line containing the Rdpack::Rdpack_bibstyles call to it.

After installling/reloading your package the lists of references should appear with long author names. "Rdpack" itself now uses this style.

Troubleshooting

A puzzling message in devtools development mode

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 and can be ignored — the help pages are built properly and no warnings appear outside developer's mode, e.g. in a separate R session¹. Even better, use the function viewRd() described below to view the required help file.

Typical errors

The functions underlying the processing of references and citations intercept errors, such as missing BibTeX labels or badly formed items in REFERENCES.bib, and issue informative warnings during the building and installation of the package, so that the developer is alerted but the package can still be built and installed. In these cases the functions usually insert a suitable text in the documentation, as well. If you encounter a situation contradicting this description, it is probably a bug — please report it (but check first for the typical errors listed below).

A non-decipherable error message is probably caused by one of the following typical errors:

• misspelled RdMacros: field in file DESCRIPTION. The safest way to avoid this is to copy it from the DESCRIPTION file of a working package.

• omitted second argument of a reference or citation macro. Most of these macros have the package name as a second argument.

These errors occur during parsing of the Rd files, before the control is passed to the Rdpack's macros.

Latex markup in BibTeX entries

In principle, BibTeX entries may contain arbitrary Latex markup, while the Rd format supports only a subset. As a consequence, some BibTeX entries may need some editing when included in REFERENCES.bib². Only do this for entries that do not render properly or cause errors, since most of the time this should not be necessary.

If mathematics doesn't render properly replace the Latex dollar syntax with Rd's \eqn, e.g. $x^2$ with \eqn{x^2}. This should not be needed for versions of Rdpack 0.8-4 or later.

Some Latex macros may have to be removed or replaced with suitable Rd markup. Again, do this only if they cause problems, since some are supported, e.g. \doi.

See also the overview help page, help("Rdpack-package"), of package "Rdpack". Among other things, it contains some dummy references which illustrate the above.

Encoding of file REFERENCES.bib

If a package has a declared encoding (in file DESCRIPTION), REFERENCES.bib is read-in with that encoding³. Otherwise, the encoding of REFERENCES.bib is assumed to be UTF-8 (which includes ASCII as a subset).

Note that BibTeX entries downloaded from online databases and similar sources may contain unexpected characters in other encodings, e.g. 'latin1'. In such cases the check tools in R-devel (since about 2018-10-01) may give warnings like:

prepare_Rd: input string 1 is invalid in this locale

To resolve this, convert the file to the declared encoding or UTF-8. Alternatively, replace the offending symbols with their classic TeX/LaTeX equivalents (which are ASCII). Non-ASCII symbols in BibTeX entries obtained from online databases are often in fields like "Abstract", which are normally not included in lists of references and can be deleted from REFERENCES.bib.

One way to check for non-ASCII symbols in a file is tools::showNonASCIIfile().

Internally, LaTeX sequences standing for accented Latin characters, such as \'e and \"o, are converted to UTF-8. So, even if the file REFERENCES.bib is pure ASCII, it may implicitly give raise to non-ASCII characters. This may cause R's checking tools to complain about non-ASCII characters even after it has been verified that there are none. If this happens, add the encoding declaration to file DESCRIPTION⁴:

Encoding: UTF-8

Needless to say, make sure that there are really no characters from encodings like 'latin1'.

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")

viewRd() renders references and citations correctly, since it understands Rd macros.

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

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.

Inserting evaluated examples

Rdpack provides a macro that takes a chunk of R code, evaluates it, and includes both the code and the results in the rendered documentation. The layout is similar to that in the R console but the code is not prefixed with anything and the output is prefixed with comment symbols. For example,

\printExample{2+2; a <- 2*3; a}

gives

2 + 2
##: 4
a <- 2 * 3
a
##: 6

The help page of ?Rdpack::promptUsage contains a number of examples created with \printExample. The corresponding Rd file can be obtained from the package tarball or from https://github.com/GeoBosh/Rdpack/blob/master/man/promptUsage.Rd.

Vignette Inserting_figures_and_evaluated_examples gives further details.

Evaluating the examples in section Examples

The macro \runExamples can be used as a replacement of section examples. For example, if the following code is put at the top level in an Rd file (i.e. not in a section):

\runExamples{2+2; a <- 2*3; a}

then it will be evaluated and replaced by a normal section examples:

\examples{
2 + 2
##: 4
a <- 2 * 3
a
##: 6
}

This generated examples section is processed by the standard R tools (almost) as if it was there from the outset. In particular, the examples are run by the R's quality control tools and tangled along with examples in other documentation files⁵. A small example package using this feature is at runExamplesCheck.

Inserting figures/graphs/plots

Figures can be inserted with the help of the standard Rd markup command \figure. To generate figures on the fly, package "Rdpack" provides the Rd macro \insertFig which takes a snipped of R code, evaluates it and inserts the plot produced by it (using \figure). \insertFig takes three arguments: a filename, the package name and the code to evaluate to produce the figure. For example,

\insertFig{cars.png}{mypackage}{x <- cars$speed; y <- cars$dist; plot(x,y)}

will evaluate the code, save the graph in file "man/figures/cars.png" subdirectory of package "mypackage", and include the figure using \figure.

See vignette Inserting_figures_and_evaluated_examples for more details.

Versions of Rdpack

Versions of Rdpack on Github are almost always fully functional (at least passing R CMD check --as-cran), and so use a three-part version number. If a version is really unstable, I would use the conventional fourth part .9000. For release on CRAN, the version is incremented to x.x.0⁶.

Note that if Rdpack (>= x.x.0) is required, it can be abbreviated to Rdpack (>= x.x).

Footnotes

¹ 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.

² Thanks to Michael Dewey for suggesting the discussion of this.

³ From Rdpack (>=0.9-1) The issue of not handling the encoding was raised by Professor Brian Ripley.

⁴ Admittedly, this is not ideal since the user should not need to care how things are processed internally but I haven't pinpointed the exact cause for this.

⁵ In versions of R before 3.6.0 the macro \runExamples may cause R CMD check to give a warning warning about unknown \Sexpr section at top level.

⁶ I adopted this versionning scheme from Rdpack 0.7.0.