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.
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
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