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
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PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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--
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
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