Organize, document and share research data and codes using R

Organize, document and share research data and codes using R

How to organize, document and share a Research Compendium

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Emerson M. Del Ponte

December 11, 2019
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  1. Organize, document and share research data and codes using Emerson

    Del Ponte Prof. of Plant Pathology Editor in Chief TPP Co-founder OPP Prepared for: Re:produce workshop Session 5: Open data, materials and code 11 Dec 2019
  2. www.openplantpathology.org

  3. Research cycle Idea Register (proposal) Run experiments Get data Analyze

    Communicate
  4. Research → Scientific Paper Idea Register (proposal) Run experiments Get

    data Analyze Communicate
  5. Is the extra effort worth it ? Organizing, Documenting and

    Sharing (Openly) Research Data and Codes
  6. Information Reproducible pen Research Practices Data Protocols Codes Share Why?

    How?
  7. Accessibility Efficiency Transparency Reproducibility Reusability Reliability Data Protocols Codes Organizing

    Documenting Sharing
  8. Get data General-purposes repositories Close/Open your data?

  9. Run experiments Close/Open your protocol?

  10. Analyse Research Compendium Close/open code?

  11. Communicate Abstract Close/open your findings? Preprint Quick Files Talk Poster

    OA paper Paywalled paper
  12. Do you WANT to change and be open? Challenging! Knowledge

    Technology
  13. Software Workflows Environments Collaborative & sharing platforms Learn: technology for

    productivity
  14. Start small… then GROW Article only Article (+ preprint) Supplemental

    (zip) - Protocols - Data Article + preprint Repository (citable) - Protocols - Data - Code Article + preprint Research compendium - Raw Data - Clean Data - Analysis (reproducible) eproducible research level 1 2 3 0
  15. http://inundata.org/talks/rstd19/ https://research-compendium.science/ Source: https://research-compendium.science/

  16. Data wrangling - Excel Data visualization - Excel Data analysis

    - SAS, STATA Scientific plots - SigmaPlot Text editor - MSWord BIB Save money! Use R and Friends
  17. How to build a RC in R? Project template package

    Manually Semi-automated Automated Creation
  18. Creation of RC project templates Manually (DIY) Semi-automated Automated "The

    workflowr R package helps researchers organize their analyses in a way that promotes effective project management, reproducibility, collaboration, and sharing of results" https://github.com/jdblischak/workflowr
  19. Project templates + website

  20. https://www.tandfonline.com/doi/full/10.1080/00031305.2017.1375986 https://peerj.com/preprints/3192/ RC as an R package

  21. Manually (RStudio) creating a as R package

  22. rrtools, an R package to create RC as package! https://github.com/benmarwick/rrtools

  23. rrtools, pkg to facilitate creation of RC as a pkg!

  24. Automating RC website creation Organized • Provides a project template

    with organized subdirectories • Mixes code and results with R Markdown Reproducible • Displays the code version used to create each result • Runs each analysis in an isolated R session ◦ Records the session information of each analysis ◦ Sets the same seed for random number generation for each analysis Shareable ◦ Creates a website to present your research results ◦ Documents how to host your website for free via GitHub Pages or GitLab Pages ◦ Creates links to past versions of results https://jdblischak.github.io/workflowr
  25. Workflowr R package https:/ /jdblischak.github.io/workflowr/articles/wflow-01-getting-started.html

  26. Reproducible for future? "holepunch will read the contents of your

    R project on GitHub... write a Dockerfile, add a badge to your README, and build a Docker image. .. dropped into a free, live, RStudio server.." https://karthik.github.io/holepunch/
  27. https:/ /github.com/emdelponte/RC-template Example RC template + holepunch Live examples: https://emdelponte.github.io/paper-FHB-Brazil-meta-analysis/

    https://emdelponte.github.io/paper-fungicides-whitemold/ https://mladencucak.github.io/AnalysisPLBIreland/index.html
  28. Example RC template + holepunch

  29. Example RC template + holepunch

  30. How to master to create and share RC?

  31. emdelponte https://osf.io/jb6yd/ Emerson_Del_Ponte edelponte emdelponte