[R] Citing R in journal articles (or the failure to)

[Achim Zeileis]

On Wed, 12 Nov 2008, Michael Friendly wrote:

>> One could complement that by a
>>   url = {http://CRAN.R-project.org/package=tweedie}
>
> In two recent in press articles where I cited R packages,
> I was asked by the copy-editor to add a location or url to the references. 
> Could I suggest that citation() be modified to include
> the URL automatically?

That's a good suggestion and one that I discussed several times with Kurt. 
The problem is that citation() only looks at the installed package which 
doesn't know where it came from. Thus, I have AFAIK no simple means of 
checking whether a particular package I'm using was obtained from CRAN, 
Bioc, R-Forge, or some local source package. Hence, the URL cannot be 
included automatically.

I agree that this would be nice to have. One idea would be that the CRAN 
maintainer adds a line to the DESCRIPTION file upon release to CRAN. There 
are a few ideas how to do this exactly and it's not yet implemented.

As a package maintainer, however, you can improve the situation for your 
own packages by writing a CITATION file that has the CRAN URL in it. For 
example, the first citEntry() in the "colorspace" package has:

## R >= 2.8.0 passes package metadata to citation().
if(!exists("meta") || is.null(meta)) meta <- 
packageDescription("colorspace")
year <- sub("-.*", "", meta$Date)
note <- sprintf("R package version %s", meta$Version)

citEntry(entry = "Manual",
          title = "{colorspace}: Color Space Manipulation",
          author = personList(as.person("Ross Ihaka"),
 	                     as.person("Paul Murrell"),
                              as.person("Kurt Hornik"),
 			     as.person("Achim Zeileis")),
          year = year,
          note = note,
          url = "http://CRAN.R-project.org/package=colorspace",

          textVersion =
          paste("Ross Ihaka, Paul Murrell, Kurt Hornik, Achim Zeileis",
    	       sprintf("(%s).", year),
                "colorspace: Color Space Manipulation.",
 	       paste(note, ".", sep = ""),
                "URL http://CRAN.R-project.org/package=colorspace")
)

Best wishes,
Z

> In the function, this would entail replacing the line
>
>  z$url <- meta$URL
>
> with something like
>
>  z$url <- if (is.null(meta$URL) paste("http://CRAN.R-project.org/package=", 
> package, sep="") else meta$URL
>
> I say "something like" because I'm not sure how to handle other repositories.
>
> Along similar lines, someone recently posted a script to generate
> a .bib file for all packages installed.  It would be useful if someone
> were to implement that script for CRAN and make the resulting
> R-packages.bib file available on the CRAN site.
>
> -Michael
>
>
> -- 
> Michael Friendly     Email: friendly AT yorku DOT ca
> Professor, Psychology Dept.
> York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
> 4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
> Toronto, ONT  M3J 1P3 CANADA
>
>
>