cboettig / knitcitations

:package: Generate citations for knitr markdown and html files
http://carlboettiger.info
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Extra output with bibliography(style="html") #20

Closed jeffjjohnston closed 11 years ago

jeffjjohnston commented 11 years ago

Using the version currently on CRAN (0.3-2), bibliography(style="html") outputs both the HTML-formatted as well as the unformatted text:

library(knitcitations)
Loading required package: knitr
Loading required package: bibtex
cleanbib()
citep("10.1038/nature09715")
[1] "Graveley _et. al._ 2010"
bibliography()
Graveley B, Brooks A, Carlson J, Duff M, Landolin J, Yang L, Artieri C, van Baren M, Boley N, Booth B, Brown J, Cherbas L, Davis C, Dobin A, Li
R, Lin W, Malone J, Mattiuzzo N, Miller D, Sturgill D, Tuch B, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green R, Hammonds A, Jiang
L, Kapranov P, Langton L, Perrimon N, Sandler J, Wan K, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel P, Brenner S, Brent M, Cherbas P,
Gingeras T, Hoskins R, Kaufman T, Oliver B and Celniker S (2010). “The Developmental Transcriptome of Drosophila Melanogaster.” _Nature_,
*471*. ISSN 0028-0836, <URL: http://dx.doi.org/10.1038/nature09715>.
bibliography(style="html")
<p>Graveley B, Brooks A, Carlson J, Duff M, Landolin J, Yang L, Artieri C, van Baren M, Boley N, Booth B, Brown J, Cherbas L, Davis C, Dobin A, Li R, Lin W, Malone J, Mattiuzzo N, Miller D, Sturgill D, Tuch B, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green R, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler J, Wan K, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel P, Brenner S, Brent M, Cherbas P, Gingeras T, Hoskins R, Kaufman T, Oliver B and Celniker S (2010).
&ldquo;The Developmental Transcriptome of Drosophila Melanogaster.&rdquo;
<EM>Nature</EM>, <B>471</B>.
ISSN 0028-0836, <a href="http://dx.doi.org/10.1038/nature09715">http://dx.doi.org/10.1038/nature09715</a>.
Graveley B, Brooks A, Carlson J, Duff M, Landolin J, Yang L, Artieri C, van Baren M, Boley N, Booth B, Brown J, Cherbas L, Davis C, Dobin A, Li
R, Lin W, Malone J, Mattiuzzo N, Miller D, Sturgill D, Tuch B, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green R, Hammonds A, Jiang
L, Kapranov P, Langton L, Perrimon N, Sandler J, Wan K, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel P, Brenner S, Brent M, Cherbas P,
Gingeras T, Hoskins R, Kaufman T, Oliver B and Celniker S (2010). “The Developmental Transcriptome of Drosophila Melanogaster.” _Nature_,
*471*. ISSN 0028-0836, <URL: http://dx.doi.org/10.1038/nature09715>.
sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] knitcitations_0.3-2 bibtex_0.3-5        knitr_1.0.5        

loaded via a namespace (and not attached):
[1] digest_0.6.2   evaluate_0.4.3 formatR_0.7    RCurl_1.95-3   stringr_0.6.2  tools_2.15.2   XML_3.95-0.1   xtable_1.7-0  
cboettig commented 11 years ago

Thanks for catching that and for the thorough issue report. It should be fixed by my last push. (Which also adds the option of bibliography("markdown").)