Editing Advanced Computational Communication Methods (Summer 2023) (section)

== Week 3: Reproducible Research II (May 30) ==


'''Resources:'''
* Blog post: [http://datasci.kitzes.com/lessons/python/reproducible_workflow.html Reproducible Workflows] by Justin Kitzes
* [https://www.youtube.com/watch?v=r9PWnEmz_tc Introduction to Snakemake Tutorial (video)]
* [https://lachlandeer.github.io/snakemake-econ-r-tutorial/index.html An Introduction to Snakemake for social science]
* [https://www.youtube.com/watch?v=zqQM66uAig0 LaTeX introduction (video)]
* [https://www.overleaf.com/learn/latex/Knitr knitr introduction]

'''Slides:'''

* [https://jeremydfoote.com/computational_communication_resources/reproducible_research/lecture/reproducible_research.html Week 2 and 3 slides]
* [https://purdue.brightspace.com/d2l/le/content/798129/viewContent/13254014/View Video of class meeting]


=== Reproducible analyses and papers ===


Key ideas:
* Some big benefits (and some drawbacks) to using text-based tools ([https://bookdown.org/yihui/rmarkdown-cookbook/ Markdown] or [https://www.overleaf.com/ LaTeX])
** Can be put in version control
** Tools like [https://yihui.org/knitr/ knitr] can be used to put code directly into a document
* Make figure creation part of your workflow, have documents point to your figures directory
* Use citation management software that integrates with your document (use [https://www.zotero.org/ Zotero])


=== Sharing ===

Key ideas:
* Share your code and data whenever possible!
* Lots of options - [https://osf.io/ OSF.io], [https://dataverse.harvard.edu/ Harvard Dataverse], etc. 
* Share preprints online



=== Advanced: Workflow Management ===

Key ideas:
* Tools to reproduce as much of the workflow as possible
* README file is much better than nothing
* Even better is a "wrapper" script that runs everything
** Very clear exactly what is run and how
** Some fairly simple options:
*** Python file
*** [https://www.gnu.org/software/make/ GNU Make]
*** [https://snakemake.github.io/ Snakemake]