Linking to other packages in documentation in roxygen2 in R

Question

I am wondering it there exists a method to link to function from other package when I'm trying to write a documentation for new package using roxygen2. Something like \link{pck=PACKAGE_NAME, fun=FUNCTION_NAME}?

Exploratory

Try \code{\link[MASS]{stats}}, from here (scroll way down). – Parlor

Thanks. Mb you know where could I find a full list of roxygen2 documentation parameters like what's stand for @param or @family or so on? There are many that I couldn't find info about them anywhere. For example: – Exploratory

roxygen2 now supports the more convenient [MASS::stats()] which evaluates to \link[MASS]{stats} when roxygen creates the .Rd files. – Keratose

Answer 1

You have to type \link[pkg]{function} e.g. \link[stringi]{stri_c}

Tellez

so short answer but so valuable :) – Exploratory

note chapter "alternative documentation workflow" in hadley's book. In order to see the links, you have to rebuild the package, not only re-document. – Sabbatarian

Answer 2

Roxygen2 now also supports documentation written in markdown.

The markdown syntax is for the link is [foo::bar()] which is translated to \code{\link[foo:bar]{foo::bar()}} in the generated .Rd file. (See Roxygen2 vignette.)

Note that you may need to specifically turn on Markdown support by writing Roxygen: list(markdown = TRUE) in your DESCRIPTION file, or by putting an #' @md comment if you want to enable markdown only for a specific man page. This is also explained at the very top of the linked vignette. (Thanks to @Tjebo for the comment)

Note that there are two colons in the markdown version whereas there is only one colon in the Rd version.

Infamy

Wow, amazing!! Thanks – Exploratory

Thank you for the note about enabling markdown! I've seen recommendations elsewhere about using markdown style links and was infuriated when I couldn't get them to work :facepalm: – Retrocede

You can convert existing documentation using roxygen2md::roxygen2md(). – Antonio

Answer 3

There are two ways to achieve this, using:

1. .Rd syntax

From "R packages" book:

• \code{\link{function}} - function in this package.
• \code{\link[MASS]{abbey}} - function in another package.
• \link[=dest]{name} - link to dest, but show name.
• \code{\link[MASS:abbey]{name}} - link to function in another package, but show name.
• \linkS4class{abc} - link to an S4 class.

2. markdown syntax

From roxygen2 vignette

roxygen2 comment	description	generated Rd code
[func()]	func() in this package	\code{\link[=func]{func()}}
[pkg::func()]	func() in the pkg	\code{\link[pkg:func]{pkg::func()}}
[thing]	topic in this package	\link{thing}
[pkg::thing]	topic in the pkg	\link[pkg:thing]{pkg::thing}
[`thing`]	topic in this package	\code{\link{thing}}
[`pkg::thing`]	topic in the pkg	\code{\link[pkg:thing]{pkg::thing}}

Remember to put Roxygen: list(markdown = TRUE) in the DESCRIPTION
Markdown shortcodes available from roxygen2>=6.0.0

Bim

Is there any way to link to another (complete) package? – Pashm

@Pashm see here #70654891 – Bim

If you want another link text, use e.g. [`dgCMatrix`][Matrix::dgCMatrix-class] – Backsight

Answer 4

In addition to the answer by potockan:
Some packages document several functions in a single help page. For example, the trim function from Bioconductor package GenomicRanges is documented in intra-range-methods (which is also the name of a help page from other packages such as IRanges).

To link to the right page with roxygen2 you can use:

\link[GenomicRanges:intra-range-methods]{trim} 

or

\code{\link[GenomicRanges:intra-range-methods]{trim}}  

to format the text correctly.

The help page will only show trim but will link to the right help page.

Spinoza

This was helpful when I wanted to link to the dplyr dplyr_tidy_seelct page. \code{\link[dplyr::dplyr_tidy_select]{tidy-select} resulted in a warning and broken link, but \code{\link[dplyr:dplyr_tidy_select]{tidy-select} worked. – Antonio

Answer 5

To link to a function, we slightly abuse markdown syntax by using [function()] or [pkg::function()].

• Re-document your package by pressing Cmd/Ctrl + Shift + D.

• Build and install your package by clicking in the build pane or by pressing Ctrl/Cmd + Shift + B. This installs it in your regular library, then restarts R and reloads your package.

• Preview documentation with ?

Mishandle