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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

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

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  2. www.openplantpathology.org

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

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

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  5. Is the extra effort worth it ?
    Organizing, Documenting and Sharing (Openly) Research Data and Codes

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  6. Information
    Reproducible
    pen
    Research Practices
    Data
    Protocols
    Codes
    Share
    Why?
    How?

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  7. Accessibility
    Efficiency
    Transparency
    Reproducibility
    Reusability
    Reliability
    Data
    Protocols
    Codes
    Organizing
    Documenting
    Sharing

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

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  9. Run experiments
    Close/Open your protocol?

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  10. Analyse Research Compendium
    Close/open code?

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

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  12. Do you WANT to change and be open?
    Challenging!
    Knowledge
    Technology

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

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  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

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  15. http://inundata.org/talks/rstd19/
    https://research-compendium.science/
    Source:
    https://research-compendium.science/

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  16. Data wrangling - Excel
    Data visualization - Excel
    Data analysis - SAS, STATA
    Scientific plots - SigmaPlot
    Text editor - MSWord
    BIB
    Save money! Use R and Friends

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  17. How to build a RC in R?
    Project template package
    Manually Semi-automated
    Automated
    Creation

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  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

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  19. Project templates + website

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

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  21. Manually (RStudio)
    creating a as R package

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

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

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  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

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  25. Workflowr R package
    https:/
    /jdblischak.github.io/workflowr/articles/wflow-01-getting-started.html

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  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/

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  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

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  28. Example RC template + holepunch

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  29. Example RC template + holepunch

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  30. How to master to create and share RC?

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

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