From mtmorgan at fhcrc.org  Fri May 23 15:42:43 2014
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Fri, 23 May 2014 06:42:43 -0700
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: <537F5053.8090003@fhcrc.org>

On 05/23/2014 05:35 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.

Thanks for clarifying. For what it's worth, I was aiming for

     print(b, style="html")

>> 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.
>
> 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,

Yes, that helps a lot, thanks,

Martin

> 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
>>


-- 
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



[Rd] citEntry handling of encoded URLs
Martin Morgan