Know your R usage workflow to handle reproducibility challenges
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The document discusses reproducibility challenges faced by R programmers, illustrated through the experiences of users having compatibility issues with R packages. It defines reproducibility as the ability to consistently execute code across different environments and highlights three suggested workflows to address these challenges. Additionally, it recommends using Docker for development and deployment to manage package versions and configurations efficiently.
Know your R usage workflow to handle reproducibility challenges
- 1. Copyright (c) WLOG Solutions Know your R usage workflow to handle reproducibility challenges Budapest, 2018
- 2. Copyright (c) WLOG Solutions Kate and Henry Freelancer/scientist/ consultant The Team Corporate/ In-house team Meet Personas John Student/hobbyist
- 3. Copyright (c) WLOG Solutions They were coding in R happily until that one day...
- 4. Copyright (c) WLOG Solutions https://xkcd.com/234/
- 5. Copyright (c) WLOG Solutions John Could not deliver R labs homework due to package incompatibility at professors laptop.
- 6. Copyright (c) WLOG Solutions Kate and Henry Missed deadlines due to problems installing packages for their R shiny app at Customer’s Server running RedHat Enterprise 6.8.
- 7. Copyright (c) WLOG Solutions The Team Had serious issues with package versions conflicts due to many users, many projects, running RedHat Enteprise machine without internet access.
- 8. Copyright (c) WLOG Solutions Three different stories the same reproducibility problem.
- 9. Copyright (c) WLOG Solutions What is reproducibility?
- 10. Copyright (c) WLOG Solutions Reproducibility is the ability to run your code repeatedly, at different time, using different computer, in such way to obtain the same outputs given the same inputs.
- 11. Copyright (c) WLOG Solutions Reproducibility is the ability to run a code repeatedly, at different time, using different computer, in such way to obtain the same outputs given the same inputs.
- 12. Copyright (c) WLOG Solutions Reproducibility is the ability to run your code repeatedly, at different time, using different computer, in such way to obtain the same outputs given the same inputs.
- 13. Copyright (c) WLOG Solutions Reproducibility is the ability to run your code repeatedly, at different time, at different computer, in such way to obtain the same outputs given the same inputs.
- 14. Copyright (c) WLOG Solutions Reproducibility is the ability to run your code repeatedly, at different time, using different computer, in such way to obtain the same outputs given the same inputs.
- 15. Copyright (c) WLOG Solutions Bare metal Operating system Solution dependencies Code Data
- 16. Copyright (c) WLOG Solutions Few examples
- 17. Copyright (c) WLOG Solutions 17 forecast v7.2 - ggplot2 (>= 2.0.0) - Rcpp (>= 0.11) - Added gglagplot R 3.3.1 2016-01-03 2016-09-08 forecast v6.2 - Rcpp (>= 0.11) R 3.2.3 forecast v8.0 - ggplot2 (>= 2.0.0) - Rcpp (>= 0.11) - Modified defaults for gglagplot R 3.3.2 2017-03-01
- 18. Copyright (c) WLOG Solutions 18
- 19. Copyright (c) WLOG Solutions Development Production
- 20. Copyright (c) WLOG Solutions I recommend using rocker/r-ver
- 21. Copyright (c) WLOG Solutions When is reproducibility important while you program in R?
- 22. Copyright (c) WLOG Solutions Debian/Ubuntu RedHat/Centos Windows Debian/Ubuntu RedHat/Centos Windows Development Production Deploy (share) solution to production
- 23. Copyright (c) WLOG Solutions Debian/Ubuntu RedHat/Centos Windows Debian/Ubuntu RedHat/Centos Windows Development Development’ Restore development environment
- 24. Copyright (c) WLOG Solutions Three workflows three reproducibility solutions.
- 25. Copyright (c) WLOG Solutions John, student/hobbyist Dev/Production Version controlFamily&Friends or Professor MRAN
- 26. Copyright (c) WLOG Solutions Kate and Henry, consultancy team/freelancer/scientist DevProduction Continuous integration Version control Local CRAN MRAN On-premise Cloud Spark etc.
- 27. Copyright (c) WLOG Solutions The Team, corporate/in-house team DevProduction Continuous integration Version control Local CRAN
- 28. Copyright (c) WLOG Solutions One word on Docker Development Production Build for different OS Deployment package . zip
- 29. Copyright (c) WLOG Solutions Second word on Docker Development Production Build Docker image
- 30. Copyright (c) WLOG Solutions CRAN management Multiple R versions Debian/Ubuntu Windows RedHat/CenOS Docker Jenkins Isolated projects http://rsuite.io https://github.com/WLOGSolutions/RSuite https://www.slideshare.net/WLOGSolutions No installation on prod Internetless environments System requirements Git/SVN Binary packages