From murdoch.duncan at gmail.com  Fri May 23 17:38:12 2014
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Fri, 23 May 2014 11:38:12 -0400
Subject: [Rd] citEntry handling of encoded URLs
In-Reply-To: <alpine.DEB.2.10.1405231410130.30578@paninaro.uibk.ac.at>
References: <537E7FC9.7030408@fhcrc.org>
	<alpine.DEB.2.10.1405231410130.30578@paninaro.uibk.ac.at>
Message-ID: <537F6B64.8020303@gmail.com>

On 23/05/2014 8:35 AM, Achim Zeileis wrote:
> On Thu, 22 May 2014, Martin Morgan wrote:
>
> > The following citEntry includes a url with %3A and other encodings
> >
> > citEntry(entry="article",
> >         title = "Software for Computing and Annotating Genomic Ranges",
> >         author = personList( as.person("Michael Lawrence" )),
> >         year = 2013,
> >         journal = "{PLoS} Computational Biology",
> >         volume = "9",
> >         issue = "8",
> >         doi = "10.1371/journal.pcbi.1003118",
> >         url =
> > "http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118",
> >         textVersion = "Lawrence M..." )
> >
> > Evaluating this as R code doesn't parse correctly and generates a warning
>
> The citEntry (or bibentry) itself is parsed without problem. Some printing
> styles cause the warning, specifically when the Rd parser is used for
> formatting. Depending on how you want to print it, the warning doesn't
> occur though. Using bibentry() directly, we can do:
>
> b <- bibentry("Article",
>     title = "Software for Computing and Annotating Genomic Ranges",
>     author = "Michael Lawrence and others",
>     year = "2013",
>     journal = "PLoS Comptuational Biology",
>     volume = "9",
>     number = "8",
>     doi = "10.1371/journal.pcbi.1003118",
>     url = "http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118",
>     textVersion = "Lawrence M et al. (2013) ..."
> )
>
> Then the default
>
> print(b)
>
> issues a warning because the Rd parser thinks that the % are comments.
> However,
>
> print(b, style = "BibTeX")
> print(b, style = "citation")
>
> don't issue warnings and also produce output that one might expect.
>
> > A work-around is, apparently, to quote the %, \\%3A etc., but is this the
> > intention?
>
> In that case the default print(b) yields the desired output without
> warning but print(b, style = "BibTeX") or print(b, style = "citation") are
> possibly not in the desired format. I'm not sure though how the different
> BibTeX style files actually handle the URLs. I think some .bst files
> handle the "url" field verbatim (i.e., don't need escaping) while others
> treat it as text (i.e., need escaping). Personally, I would hence avoid
> the problem and only use the DOI URL here as this will be robust across
> BibTeX styles.
>
> Nevertheless it is not ideal that there is a discrepancy between the
> different printing styles. I think currently this can only be avoided if
> custom macros are employed. But Duncan might be able to say more about
> this. A similar situation occurs if you use commands that are not part of
> the Rd markup, e.g.

I'd go further than "not ideal", I think we need to define what kind of 
markup is permissible in this context.  If it needs to be Rd markup, 
then the default print method should be fixed to hide it (and \mathcal 
should not be allowed); if it needs to be plain text, then some escaping 
should be done.

>
> n01 <- bibentry("Misc", title = "The $\\mathcal{N}(0, 1)$ Distribution",
>     author = "Foo Bar", year = "2014")
> print(n01) # warning
> print(n01, style = "BibTeX") # ok
>
> > Also, citEntry points to bibentry points to *Entry Fields*, but the
> > 'url' tag is not mentioned there, even though url appears in the
> > examples; if the list of supported tags is not easy to enumerate,
> > perhaps some insight can be provided at this point as to how the
> > supported tags are determined?
>
> This follows the BibTeX conventions. Thus, you can use any tag that you
> wish to use and it will depend on the style whether it is displayed or
> not. The only restriction is that certain bibtypes require certain
> fields, e.g., an "Article" has to specify: author, title, journal, year.
> But beyond that you can add any additional field. For example, in your
> bibentry above you used the "issue" field which is ignored by most BibTeX
> styles. My adaptation uses the "number" field instead which is processed
> by most standard BibTeX styles.
>
> The default print(..., style = "text") uses a bibstyle that is modeled
> after jss.bst, the BibTeX style employed by the Journal of Statistical
> Software. But you could plug in other .bibstyle arguments, e.g. one that
> processes the "issue" field etc.
>
> Hope that helps,
> Z
>
> > Thanks
> >
> > Martin Morgan
> > --
> > Computational Biology / Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N.
> > PO Box 19024 Seattle, WA 98109
> >
> > Location: Arnold Building M1 B861
> > Phone: (206) 667-2793
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
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[Rd] citEntry handling of encoded URLs
Duncan Murdoch