Writing Manifesto

Notes on Using Authorea for Collaboration

First, a personal manifesto while waiting forhte first rays fo the day to come: I have decided to publish in Open Access publications as far as practicable (at least for those where I am the prinicpal author), use preprints exclusively for my presentations and all my publications and distribute the URLs of my preprints to my colleagues and students, and friends and network in academic media, and use plain text and web based writing media as far as practical. For other tools, the idea is a little divided. I prefer to use Open Access R for my research, and use LaTeX for my academic writing including slide production in Beamer, but these are not always possible. I also use and actually encourage people to use Stata for statistical data analysis, so the landscape is mixed. However, for publishing my work, I am increasingly leaning towards using collaboative publishing units such as Overleaf and Authorea, and use the PeerJ preprint servers, so I believe it’s a good time to write a few notes about these tools here. As the bibliography format is largely BibTeX, it does not matter what software I use, but I use Sente, but others can as easily be used. I have also started learning Python and use iPython notebooks, specifically using one at Wakari.io,and Juliabox, so these will come on as well.

Workflow I follow

Apply for funding –> fail/pass, do Research (some primary data analysis, some secondary data analysis and meta analysis) –> publish, teaching –> publish, and collaborate. Develop first drafts in Authorea, and then distribute as preprints for further soliciiting responses from colleagues and critics before sending it out for publishing.

Not all colleagues will understand the weight of plain text or will prefer Word. What then? Send them RTF converted or HTML converted files, take in their word marks and then incorporate and send out incorporating their changes, highlighting back to them (along with notes). More work, but worth it, and shows that I care for the changes that they have want me to work on. Also, keep everything on Authorea and invite them. What if Authorea dies? Or what if, overleaf dies? Keep the same process, but keep working in LaTeX document. If LaTeX is hard to learn, learn. It cannot be that bad.

Notes on Authorea

Authorea is intuitive. Basically start with a free account and start writing. There are a few minor tweaks that can make your life a lot easier to work with this medium though and save frustrations.

  1. Writing is simple, just plain text with markdown, and markdown is gorgeous. It has three levels of headings, bold, italic, support, standard table support (ideally markdown tables are good, and these can usually be prepared easily in the app itself). I prefer to wrie using markdown as this format is simple easy and intuitive. But it is possible to write using LaTeX as well.
  2. Add figures next to the text chunks.
  3. Speaking of chunks, it makes sense then to analyse everything in either R or Stata and then output in LaTeX and write back in Authorea.
  4. Create separate foo.tex files and add them to Authorea and then add the links to Authorea’s layout.md file
  5. Prepare a bibilo.bib file and keep the bibtex in it. Refer to the citations from there.
  6. Write in Scrivener and export from markdown to LaTeX and upload to Authorea for fine tuning
  7. Write in Authorea and keep copies in Github. That way, write everything in personal computer, save in a file in github
  8. Keep a copy in personal blog (this), otherwise push every large piece of thought in medium

Medium can be used for writing half finished blogs and for seeking peer review comments which can then be changed.

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