HTML or Markdown links for in-line citations

[zkamvar]

Hello,

I recently updated to the most recent version (1.0-1) and noticed that I no longer have the ability to have html links in my in-line citation. I have produced a minimal reproducible example here: https://gist.github.com/zkamvar/f9335be4aaad413fe01c where I specify

cite_options(citation_format = "pandoc", max.names = 3, 
             cite.style = "authoryear", style = "markdown", 
             hyperlink = "to.doc")

I am expecting hyperlinks on my inline citations, but they don't appear even if I select style = "html". Is there a way to add this as an option?

[cboettig]

@zkamvar Yeah, that's correct; if you use citation_format = pandoc you won't get hyperlinks. Use citation_format = "text" and it should work, but it doesn't because of a real bug this time. I believe I have just fixed that bug with the most recent push to Github (v0.1.1.99). Of course without pandoc mode you cannot benefit from CSL stylesheets...

Recall that in pandoc mode, kniticitations tells knitr to just generating citations like [@authoryear] and pandoc is responsible for formatting them from there (using the CSL stylesheet specified). Since hyperlinks are not part of the CSL stylesheet, you don't get hyperlinked references. (You would think that is something that pandoc would be able to handle, but it turns out it's not so simple. See https://groups.google.com/forum/#!msg/pandoc-discuss/0UlUwrViCOQ/KBBs-6rNvY0J)

Thanks for the bug report.

[dhimmel]

@cboettig, Thanks for creating this needed package. I first experienced the convenience of doi-only citation when writing my proposal for ThinkLab (Jesse mentioned you two had been in touch). Then I came looking for similar functionality for my html-out rmarkdown projects. I suspect doi-based citation will be the future, and I pity the publishers who still don't assign doi's to their articles.

I agree that hyperlinked inline citations are will be a major addition and provide great utility and elegance. Hopefully, some of these upstream issues get resolved.