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How to write a reproducible paper

Damien Irving
December 12, 2016

How to write a reproducible paper

Presentation from the 2016 AGU Fall Meeting in San Francisco. A more detailed account of the content presented can be found at the following blog post:

Damien Irving

December 12, 2016

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  1. How to write a reproducible paper Damien Irving Postdoctoral Research

    Fellow CSIRO Oceans and Atmosphere Hobart, Australia @DrClimate https://drclimate.wordpress.com
  2. Baker (2016). Nature 533, 452–4. doi:10.1038/533452a We don’t document our

    software and code, so it’s impossible to replicate the computational results presented in geoscience papers today
  3. Wanted: A concrete example ž I set out to write

    a reproducible paper — My background ◦ Software Carpentry instructor ◦ CSIRO support scientist ◦ Regular PyCon attendee ◦ Data science blog: drclimate.wordpress.com — Lit review ◦ Barriers to publishing code ◦ Computational best practices
  4. ž Brief overview of software packages ž Link to collection

    of supplementary materials — Code, software, processing steps — Host with Figshare / Zenodo Computation section http://dx.doi.org/10.6084/m9.figshare.1385387
  5. Code ž Minimum standard — Snapshot of code library ž

    Other options — Version control that library — Link to an external hosting service ◦ Allows readers to view updates & submit pull requests Simplest thing any author can do to ensure their results are reproducible Alternative and/or additional things that (some) authors could do to (potentially) make the reader’s life easier
  6. Software ž Minimum standard — Manual listing: name, version number,

    release date, institution and DOI or URL ž Other options — Conda – “conda env create dirving/jclimate” — Docker / Nix
  7. Processing steps ž Minimum standard: — Step-by-step account, raw data

    to result — Options depend on what software you’re using ◦ Command line log file for each figure / result ◦ Informative README file/s
  8. Processing steps ž Other options — Makefile — Workflow management

    system VisTrails provides a graphical interface to drag and drop the various components of your workflow
  9. Summary Minimum standard Other options Code Snapshot of code library*

    Version control* External hosting service* Software Name, version number, release date, institution and DOI or URL of each software package* Conda* Docker / Nix Processing steps Command line log file* README* Makefile* Workflow system *Skills can be picked up at a 2-day Software Carpentry workshop.
  10. Questions? https://drclimate.wordpress.com/2016/06/16/ how-to-write-a-reproducible-paper/ Irving D, Simmonds I (2015). A novel

    approach to diagnosing Southern Hemisphere planetary wave activity and its influence on regional climate variability. Journal of Climate. 28, 9041-57. doi:10.1175/JCLI-D-15-0287.1 Irving D (2016). A minimum standard for publishing computational results in the weather and climate sciences. Bulletin of the American Meteorological Society. 97, 1149-1158. doi:10.1175/BAMS-D-15-00010.1