Organize, document and share research data and codes using R

How to organize, document and share a Research Compendium

Transcript

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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