Better support reproducible research

Kudos on making Paperpile! It’s been fun to explore.

Reproducible research is increasingly important for many researchers, journals, and funding institutions. For example, I increasingly generate reports and even entire manuscripts using Rmarkdown files that integrate text and code.

Right now, there’s no way (I don’t think) to integrate Paperpile into a reproducible workflow. For example, using EndNote I can copy a reference from my library and paste its code into my Rmarkdown script. Then I run the script, generate a Word document using Pandoc, and run through EndNote to get formatted citations and references. A bit clunky but it works well.

So, feature request: it would be great to have this capability in Paperpile–i.e., a way to have citations to documents in my Paperpile library in an offline document that could subsequently be formatted by the Paperpile app (either locally or in an imported Google Doc). Thanks.

Thanks for trying Paperpile and coming here from Twitter. I think I now understand what you are after. It will be possible with the new Word plugin (not right away but eventually).

The thing is there are various other ways to write manuscripts these days like Scrivener, Ulysses. Those typically export to Word and we thought about how we can enable citation support with Paperpile for these products. It’s pretty much as you describe. You insert a citation code, export to word and run Paperpile.

If your input source is a text file it’s even easier because we can directly scan and replace the citations without starting word. However, I’m not sure how common the workflow is and if/when we handle this case separately.

The workflow with Word is definitely coming.

Thanks, Stefan. Just to clarify, while I mentioned Word, was thinking more generally: insert a citation code into text document, upload to Google Docs, and run Paperpile. But as you say, Word is a lingua franca and if the functionality would come through a (Mac) Word plugin, that would work fine too.

Thanks for your understanding of this issue, and for Paperpile! I’m so impressed with it.

Allow me to very lately endorse this as well. It would be very helpful to be able to have human- or machine-typable code format that Paperpile could scan and update, similar to EndNote’s “Temporary Citations” that you use when exporting.

Even better might be be using that exact format and somehow making the IDs/Labels more accessible and able to be defined across documents, perhaps allowing DOIs or PMIDs to be used for this purpose. That way `{Hosseini, 2010 10.1371/journal.pone.0012763} would work across tools and be easy too generate in plain-text.

I really hope that it will eventually be possible to work in Ulysses with temporary citations markers (from the iOS app) and upload to Google Docs for scanning…