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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
  2. Is the extra effort worth it ? Organizing, Documenting and

    Sharing (Openly) Research Data and Codes
  3. 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
  4. Data wrangling - Excel Data visualization - Excel Data analysis

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

    Manually Semi-automated Automated Creation
  6. 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
  7. 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
  8. 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/
  9. 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