Reproducible Environments in R

•

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This document discusses reproducible environments for data science projects. It describes challenges like dependency issues when moving code between systems. It recommends tools like Packrat, Checkpoint and Switchr to manage package dependencies when working with R code. Docker is presented as a way to create portable development environments using containerization. The document demos how to build a Docker container for an R project and argues containers will become more important for reproducible data science.

Data & Analytics

Doug Ashton - Consultant
dashton@mango-solutions.com
Reproducible Environments
Doug Ashton

Doug Ashton - Consultant
dashton@mango-solutions.com
Reproducible Environments
Reproducible Packages
Overview
Reproducible
Code

Doug Ashton - Consultant
dashton@mango-solutions.com
Overview

Doug Ashton - Consultant
dashton@mango-solutions.com

Doug Ashton - Consultant
dashton@mango-solutions.com
Reproducible Code

Doug Ashton - Consultant
dashton@mango-solutions.com
Can you just re-run
those numbers for
me?

Doug Ashton - Consultant
dashton@mango-solutions.com
codedata

Doug Ashton - Consultant
dashton@mango-solutions.com
Two Warnings
• Retracted cancer research –
http://bit.ly/londonr01 (video)
• Reinhart, Rogoff, and the Excel
Error That Changed History -
http://bit.ly/londonr02

Doug Ashton - Consultant
dashton@mango-solutions.com
the solution
code

Doug Ashton - Consultant
dashton@mango-solutions.com
A Reproducible Flow
RawData
Results
Script

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Demo
• https://github.com/dougmet/repEnvDemo

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Input data
Output data
Manipulation
Calculation
Dependencies
Plots

Doug Ashton - Consultant
dashton@mango-solutions.com
Reproducible Research Tools
• Knitr/Sweave
• rmarkdown
• Jupyter (Ipython) Notebook
• RCloud
• git

Doug Ashton - Consultant
dashton@mango-solutions.com
Elephant picReproducible Packages

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the new problem

Doug Ashton - Consultant
dashton@mango-solutions.com
Your Laptop

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dashton@mango-solutions.com
Their server

Doug Ashton - Consultant
dashton@mango-solutions.com
Package Versions
• Packrat/checkpoint/switchr
• MRAN mirror snapshots
• E.g. https://mran.revolutionanalytics.com/snapshot/2015-03-01
• Managed installation (validR)

Doug Ashton - Consultant
dashton@mango-solutions.com
Package Management Packages
Packages Pros Cons
Packrat Built into Rstudio Bulky in repo (eg git)
Needs foresight
Checkpoint Easy
Rescues old scripts
Lots of libraries
Only one date
Switchr Package manifests
Repo friendly
Not easy

Doug Ashton - Consultant
dashton@mango-solutions.com
Packrat

Doug Ashton - Consultant
dashton@mango-solutions.com
Checkpoint
Pros
• Get old scripts working
• Simple (just set a date)
checkpoint(“2014-11-05”)
• Downloads packages
from MRAN on that date
(more later)
Cons
• Could end up with lots of
packages (library for each
date)
• Doesn’t help with multiple
dates
• No GitHub

Doug Ashton - Consultant
dashton@mango-solutions.com
Switchr
• No demo

Doug Ashton - Consultant
dashton@mango-solutions.com
Reproducible Environments

Doug Ashton - Consultant
dashton@mango-solutions.com
Reproducible Environments
3. Scalability2. Managed
Environments
1. System Dependencies

Doug Ashton - Consultant
dashton@mango-solutions.com
Vagrant
• www.vagrantup.com
• Primarily for development
• Each project gets a virtual machine

Doug Ashton - Consultant
dashton@mango-solutions.com
Docker
• www.docker.com
• Primarily for deployment
• One VM (Windows/Mac)
• No VMs (Linux)
• Scalable

Doug Ashton - Consultant
dashton@mango-solutions.com
Docker Images are Hierachical
Ubuntu
14.04
R-base
R-Finance R-Spark
Project-X
R-Hadley
Project-Y

Doug Ashton - Consultant
dashton@mango-solutions.com
Docker Containers
Multiple
containers from
one image, launch
rapidly

Doug Ashton - Consultant
dashton@mango-solutions.com
Rocker Warning

Doug Ashton - Consultant
dashton@mango-solutions.com
Docker Demo
• https://github.com/dougmet/dockerR
FROM dougmet/r-base:3.1.2
RUN apt-get -y install libgsl0ldbl=1.16*1 libgsl0-dev=1.16*
# Install R package manifest
COPY loadPackages.R /tmp/
COPY packages.csv /tmp/
RUN Rscript /tmp/loadPackages.R
CMD ["R"]

Doug Ashton - Consultant
dashton@mango-solutions.com
The near future
• More centralised R installations
• Centralised images
• Windows containers (open container initiative)
• Data Science Workbench
• Managed image repo
• One click to open project
• RStudio integration

Doug Ashton - Consultant
dashton@mango-solutions.com
Get in touch
• GitHub
• MangoTheCat
• dougmet
• Twitter
• @dougashton
• Email
• dashton@mango-solutions.com

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Gen AI on Enterprise Cloud Apache NiFi Milvus Apache Kafka Apache Flink Cloudera Machine Learning Cloudera DataFlow https://medium.com/@tspann/building-a-milvus-connector-for-nifi-34372cb3c7fa https://www.meetup.com/futureofdata-princeton/events/300737266/ https://lu.ma/q7pcfyjn?source=post_page-----34372cb3c7fa--------------------------------&tk=TTyakY If you're interested in working with Generative AI on the cloud, this virtual workshop is for you. Tim Spann from Cloudera and Yujian Tang from Zilliz will cover how you can implement your own GenAI workflows on the cloud at enterprise scale. 9:00 - 9:05: Intro 9:05 - 9:15: What is Milvus 9:15 - 9:25: Cloudera Development Platform 9:25 - 10:00: Demo Location https://www.youtube.com/watch?v=IfWIzKsoHnA https://github.com/tspannhw/SpeakerProfile https://www.linkedin.com/in/yujiantang/

Generative AI on Enterprise Cloud with NiFi and Milvus

Timothy Spann

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Digital Advertising Lecture for Advanced Digital & Social Media Strategy at U...

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Reproducible Environments in R

1. Doug Ashton - Consultant dashton@mango-solutions.com Reproducible Environments Doug Ashton

2. Doug Ashton - Consultant dashton@mango-solutions.com Reproducible Environments Reproducible Packages Overview Reproducible Code

3. Doug Ashton - Consultant dashton@mango-solutions.com Overview

4. Doug Ashton - Consultant dashton@mango-solutions.com

5. Doug Ashton - Consultant dashton@mango-solutions.com Reproducible Code

6. Doug Ashton - Consultant dashton@mango-solutions.com Can you just re-run those numbers for me?

7. Doug Ashton - Consultant dashton@mango-solutions.com codedata

8. Doug Ashton - Consultant dashton@mango-solutions.com Two Warnings • Retracted cancer research – http://bit.ly/londonr01 (video) • Reinhart, Rogoff, and the Excel Error That Changed History - http://bit.ly/londonr02

9. Doug Ashton - Consultant dashton@mango-solutions.com the solution code

10. Doug Ashton - Consultant dashton@mango-solutions.com A Reproducible Flow RawData Results Script

11. Doug Ashton - Consultant dashton@mango-solutions.com Demo • https://github.com/dougmet/repEnvDemo

12. Doug Ashton - Consultant dashton@mango-solutions.com Input data Output data Manipulation Calculation Dependencies Plots

13. Doug Ashton - Consultant dashton@mango-solutions.com Reproducible Research Tools • Knitr/Sweave • rmarkdown • Jupyter (Ipython) Notebook • RCloud • git

14. Doug Ashton - Consultant dashton@mango-solutions.com Elephant picReproducible Packages

15. Doug Ashton - Consultant dashton@mango-solutions.com the new problem

16. Doug Ashton - Consultant dashton@mango-solutions.com Your Laptop

17. Doug Ashton - Consultant dashton@mango-solutions.com

18. Doug Ashton - Consultant dashton@mango-solutions.com Their server

19. Doug Ashton - Consultant dashton@mango-solutions.com Package Versions • Packrat/checkpoint/switchr • MRAN mirror snapshots • E.g. https://mran.revolutionanalytics.com/snapshot/2015-03-01 • Managed installation (validR)

20. Doug Ashton - Consultant dashton@mango-solutions.com Package Management Packages Packages Pros Cons Packrat Built into Rstudio Bulky in repo (eg git) Needs foresight Checkpoint Easy Rescues old scripts Lots of libraries Only one date Switchr Package manifests Repo friendly Not easy

21. Doug Ashton - Consultant dashton@mango-solutions.com Packrat

22. Doug Ashton - Consultant dashton@mango-solutions.com Checkpoint Pros • Get old scripts working • Simple (just set a date) checkpoint(“2014-11-05”) • Downloads packages from MRAN on that date (more later) Cons • Could end up with lots of packages (library for each date) • Doesn’t help with multiple dates • No GitHub

23. Doug Ashton - Consultant dashton@mango-solutions.com Switchr • No demo

24. Doug Ashton - Consultant dashton@mango-solutions.com Reproducible Environments

25. Doug Ashton - Consultant dashton@mango-solutions.com Reproducible Environments 3. Scalability2. Managed Environments 1. System Dependencies

26. Doug Ashton - Consultant dashton@mango-solutions.com Vagrant • www.vagrantup.com • Primarily for development • Each project gets a virtual machine

27. Doug Ashton - Consultant dashton@mango-solutions.com Docker • www.docker.com • Primarily for deployment • One VM (Windows/Mac) • No VMs (Linux) • Scalable

28. Doug Ashton - Consultant dashton@mango-solutions.com Docker Images are Hierachical Ubuntu 14.04 R-base R-Finance R-Spark Project-X R-Hadley Project-Y

29. Doug Ashton - Consultant dashton@mango-solutions.com Docker Containers Multiple containers from one image, launch rapidly

30. Doug Ashton - Consultant dashton@mango-solutions.com A Reproducible Flow RawData Results Script

31. Doug Ashton - Consultant dashton@mango-solutions.com Rocker Warning

32. Doug Ashton - Consultant dashton@mango-solutions.com Docker Demo • https://github.com/dougmet/dockerR FROM dougmet/r-base:3.1.2 RUN apt-get -y install libgsl0ldbl=1.16*1 libgsl0-dev=1.16* # Install R package manifest COPY loadPackages.R /tmp/ COPY packages.csv /tmp/ RUN Rscript /tmp/loadPackages.R CMD ["R"]

33. Doug Ashton - Consultant dashton@mango-solutions.com The near future • More centralised R installations • Centralised images • Windows containers (open container initiative) • Data Science Workbench • Managed image repo • One click to open project • RStudio integration

34. Doug Ashton - Consultant dashton@mango-solutions.com Get in touch • GitHub • MangoTheCat • dougmet • Twitter • @dougashton • Email • dashton@mango-solutions.com

Reproducible Environments in R

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