Have you heard of executable manuscripts or theses? Are you looking to use R markdown or LaTeX to combine text and statistical outputs? Are you still searching for the optimal way to compile reproducible documents ready for submission?
This community call is primarily designed for researchers who have already attended beginner workshops (e.g. in R markdown or LaTeX) or started to teach themselves the tools needed to create executable/reproducible manuscripts but are still wondering how to combine it all, all the way to submitting a computationally reproducible manuscript.
In this session, we will start with a brief introduction showcasing the benefits of executable research articles and the basic tools that allow us to create them. We will then watch short pre-recorded demonstrations of different workflows from RROx community members. They will share what tools they use and how these tools are combined into a reproducible pipeline to produce PDFs ready for submission. We will then invite attendees to discuss advantages and disadvantages of each workflow presented, and to share their own tips so that we can collectively define a set of best practices when it comes to producing a manuscript. Finally, we will combine information and resources shared by attendees with the accompanying notes from the demonstrators to create a reference sheet for the RROx community. RROx will then work to organise beginners and advanced workshops to teach the skills needed to implement the pipelines considered to be most efficient and reproducible.
This session will not be recorded, but the prerecorded workflow demonstrations of the workflows will be made available on the OSF repository: osf.io/prbjm. As a refresher, you can also find teaching material from the 4th Oxford | Berlin summer school on open research on the OSF repository: osf.io/8q59y. This includes workshop materials introducing R, Python, RMarkdown, LaTeX, and lecture recordings such as ‘How to write readable and sustainable code’.
Monday 8 November 2021, 3pm to 4.30pm online
Demonstrations (40 min):
· Ilse Pit – Introduction
· Charlie Rahal – workflow* 1: (Python + LaTeX + BibTeX) in PyCharm + Overleaf
· Ulrik Lyngs – workflow* 2: (R + Rmarkdown + Zotero) in RStudio + Google doc
· Adam Kenny – workflow* 3: (R + LaTeX + BibTeX) in Emacs + collaborative editing through version control system
Discussion (20 min)
Hackathon (30 min)
*The workflows are presented as: (programming language + markup language + references management) in an integrated development environment (IDE) or a text editor + a way of collaborating.
