Getting Work Done

Notebook Recap

• Notebooks are R Markdown documents + new interaction model
• Code chunks are executed individually
• Code output appears beneath the chunk and is saved with the document
• Combines iterative approach with reproducible result

If you've never used them before, watch the R Notebook Webinar

Navigation: Outline

Navigation: Jump To

Navigation: By Chunk

Navigation: Running

Output Management

Reproducibility

• Notebooks can be less reproducible than traditional R Markdown documents.
• Chunks can be run in any order.
• Chunks can access the global environment.

Simulating a Knit

Consistency

Input and Output

Input and Output

1. When you execute chunks in your notebook, the output is simultaneously displayed by RStudio and stored in a local cache in the .Rproj.user folder.
2. When you save your notebook, the output and your R Markdown document are combined into a single, self-contained .nb.html file.

Publishing

Two choices:

1. Publish the notebook file directly (HTML)
2. Render to a separate output format

Publishing: Notebook HTML

• Self-contained
• Compatible with any hosting service
• No viewer required
• Hydrates to full notebook (more on this later)

Publishing: Another Format

---
title: "A Monte-Carlo Analysis of Monte Carlo"
output:
  html_notebook: default
  pdf_document:
    fig_width: 9
    fig_height: 5
---

Understanding Multiple Formats

Publishing: RStudio Connect

• One-click publish inside your org
• Fine-grained access control
• Execute on the server
• Schedule executions

Collaborating: Plain Files

To: analyst@contoso.com
From: customer@northwind.com
I need some help with this analysis. Could you 
take a look at what I have so far?
Thanks,
Charles
[ Attachment: foo.nb.html ]

Collaborating: Execution in Reverse

Collaborating: Opening Code in RStudio

Collaborating: Opening Notebook in RStudio

Collaborating: Open Inside RStudio

Collaborating: Open Notebook

Collaborating: Version Control #1

• Add *.nb.html to your .gitignore or similar
• Check in only the .Rmd file
• All diffs are plain text
• Encourages reproducibility & independent verification of results

Collaborating: Version Control #2

• Check in the .nb.html file and the .Rmd file
• Diffs are noisier
• RStudio loads outputs from .nb.html if newer
• Outputs and inputs are versioned together
• No need to re-execute lengthy or fragile computations

Versioned Output

When a notebook is opened:

• The local cache modified time is compared to the .nb.html
• If .nb.html is older, it is ignored
• If .nb.html is newer, it replaces the local cache
• No merging or conflict management is performed!

The End