RSH HackMD - HackMD

# RSH HackMD You can use this file to write questions and comments. **To edit click top left edit button.** - Always write at the very bottom, this is easier for us to watch. - We will note here URLs that we mention during the session. - You may comment on, clean up, or answer other people's questions. - **Be respectful** and form a good community. ## Icebreaker What tool/trick you recommend to make your work/research more reproducible? - Think of your future self, code+take notes so that your future self will understand what you did - Code with more than one person, joint projects - Some means to install software libraries needed - Conda environments! ## Questions - Does reproducible also mean completely automated? If others have to be able to run the analysis, it feels like that. - automation could be bad and not explicitly specify code versions that break an analysis - - As a reviewer: do you ask for the code? Do you review the code? - I reviewed once a data+software paper and told the editor that I can review the code if they give me 2 weeks more... never heard back :) - I usually glance at the code. Once found a serious bug. - ReproHacks: - https://twitter.com/reprohack - https://reprohack.github.io/reprohack-hq/ - How do tasks to make work reproducible change given the scale of the project? LHC analysis groups won't act like a small group of ecologists. - an example: https://www.nature.com/articles/s41567-018-0342-2 - ReproHack is a great idea: journal-club but for github repro's: try to run the so called "reproducible" code shared by the authors of a paper - yes! - To make our research reproducible, do we have to be using notebooks (Rmarkdown, Jupyter, etc)? - I personally think the other way around. Full automation (no interaction) -> more reproducible The Jupyter and R Studio/renv examples (improvements welcome!): - https://github.com/bast/jupyter-binder-example - https://github.com/bast/rstudio-binder-example - https://github.com/bast/renv-binder-example Mamba: https://github.com/mamba-org/mamba - Containers allow for scaling that virtual environments do not.