R Markdown Jupyter Notebook

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Python has a similar tool to R Markdown called Jupyter Notebooks https://jupyter.org/. Like R Markdown it can handle various programming languages. It is used heavily within the scientific community. Nature’s 2018 article Why Jupyter is data scientists’ computational notebook of choice provides a good summary. The discussion below focuses on syntax for R Markdown but the arguments hold for Jupyter notebooks as well.

“Text can be added to Jupyter Notebooks using Markdown cells. You can change the cell type to Markdown by using the Cell menu, the toolbar, or the key shortcut m.Markdown is a popular markup language that is a superset of HTML. I would like to convert a rmarkdown.Rmd document to a jupyter notebook.ipynb.I found that converting from jupyter to rmd is easy using as described in reference page but for some reason (.) the.

Earlier, we discussed a basic workflow for capturing your R code where you work interactively in the console, then capture what works in the script editor. R Markdown brings together the console and the script editor, blurring the lines between interactive exploration and long-term code capture. You can rapidly iterate within a chunk, editing and re-executing with Cmd/Ctrl + Shift + Enter. When you’re happy, you move on and start a new chunk.

R Markdown is also important because it so tightly integrates prose and code. This makes it a great analysis notebook because it lets you develop code and record your thoughts. An analysis notebook shares many of the same goals as a classic lab notebook in the physical sciences. It:

  • Records what you did and why you did it. Regardless of how great yourmemory is, if you don’t record what you do, there will come a time whenyou have forgotten important details. Write them down so you don’t forget!

  • Supports rigorous thinking. You are more likely to come up with a stronganalysis if you record your thoughts as you go, and continue to reflecton them. This also saves you time when you eventually write up youranalysis to share with others.

  • Helps others understand your work. It is rare to do data analysis byyourself, and you’ll often be working as part of a team. A lab notebookhelps you share not only what you’ve done, but why you did it with yourcolleagues or lab mates.

Much of the good advice about using lab notebooks effectively can also be translated to analysis notebooks. I’ve drawn on my own experiences and Colin Purrington’s advice on lab notebooks (http://colinpurrington.com/tips/lab-notebooks) to come up with the following tips:

Tab in jupyter notebook markdownNotebook
  • Ensure each notebook has a descriptive title, an evocative filename, and afirst paragraph that briefly describes the aims of the analysis.

  • Use the YAML header date field to record the date you started working on thenotebook:

    Use ISO8601 YYYY-MM-DD format so that’s there no ambiguity. Use iteven if you don’t normally write dates that way!

  • If you spend a lot of time on an analysis idea and it turns out to be adead end, don’t delete it! Write up a brief note about why it failed andleave it in the notebook. That will help you avoid going down the samedead end when you come back to the analysis in the future.

  • Generally, you’re better off doing data entry outside of R. But if youdo need to record a small snippet of data, clearly lay it out usingtibble::tribble().

  • If you discover an error in a data file, never modify it directly, butinstead write code to correct the value. Explain why you made the fix.

  • Before you finish for the day, make sure you can knit the notebook(if you’re using caching, make sure to clear the caches). That willlet you fix any problems while the code is still fresh in your mind.

  • If you want your code to be reproducible in the long-run (i.e. so you cancome back to run it next month or next year), you’ll need to track theversions of the packages that your code uses. A rigorous approach is to usepackrat, http://rstudio.github.io/packrat/, which stores packagesin your project directory, or checkpoint,https://github.com/RevolutionAnalytics/checkpoint, which will reinstallpackages available on a specified date. A quick and dirty hack is to includea chunk that runs sessionInfo() — that won’t let you easily recreateyour packages as they are today, but at least you’ll know what they were.

  • You are going to create many, many, many analysis notebooks over the courseof your career. How are you going to organise them so you can find themagain in the future? I recommend storing them in individual projects,and coming up with a good naming scheme.

Today we’re excited to announce R Notebooks, which add a powerful notebook authoring engine to R Markdown. Notebook interfaces for data analysis have compelling advantages including the close association of code and output and the ability to intersperse narrative with computation. Notebooks are also an excellent tool for teaching and a convenient way to share analyses.

You can try out R Notebooks today in the RStudio Preview Release.

Interactive R Markdown

As an authoring format, R Markdown bears many similarities to traditional notebooks like Jupyter and Beaker. However, code in notebooks is typically executed interactively, one cell at a time, whereas code in R Markdown documents is typically executed in batch.

R Notebooks bring the interactive model of execution to your R Markdown documents, giving you the capability to work quickly and iteratively in a notebook interface without leaving behind the plain-text tools and production-quality output you’ve come to rely on from R Markdown.

Plain text representation
Same editor/tools used for R scripts
Works well with version control
Focus on production output
Output inline with code
Output cached across sessions
Share code and output in a single file
Emphasized execution modelInteractive & BatchInteractive
R Markdown NotebooksTraditional Notebooks

This video provides a bit more background and a demonstration of notebooks in action:

Jupyter Notebook Markdown Latex

[youtube https://www.youtube.com/watch?v=zNzZ1PfUDNk&w=560&h=315]

Iterate Quickly

In a typical R Markdown document, you must re-knit the document to see your changes, which can take some time if it contains non-trivial computations. R Notebooks, however, let you run code and see the results in the document immediately. They can include just about any kind of content R produces, including console output, plots, data frames, and interactive HTML widgets.

You can see the progress of the code as it runs:

You can preview the results of individual inline expressions, too:

R Markdown Jupiter Notebook Free

Even your LaTeX equations render in real-time as you type:

This focused mode of interaction doesn’t require you to keep the console, viewer, or output panes open. Everything you need is at your fingertips in the editor, reducing distractions and helping you concentrate on your analysis. When you’re done, you’ll have a formatted, reproducible record of what you’ve accomplished, with plenty of context, perfect for your own records or sharing with others.

Batteries Included

R Notebooks can run more than just R code. You can run chunks written in other languages, like Python, Bash, or C++ (Rcpp).

It’s even possible to run SQL directly:

This makes an R Notebook an excellent tool for orchestrating a reproducible, end-to-end data analysis workflow; you can easily ingest data using your tool of choice, and share data among languages by using packages like feather, or ordinary CSV files.

Reproducible Notebooks

Markdown

While you can run chunks (and even individual lines of R code!) in any order you like, a fully reproducible document must be able to be re-executed start-to-finish in a clean environment. There’s a built-in command to do this, too, so it’s easy to test your notebooks for reproducibility.

Tab In Jupyter Notebook Markdown

Rich Output Formats

Since they’re built on R Markdown, R Notebooks work seamlessly with other R Markdown output types. You can use any existing R Markdown document as a notebook, or render (knit) a notebook to any R Markdown output type.

The same document can be used as a notebook when you’re quickly iterating on ideas and later rendered to a wholly different format for publication – no duplication of code, data, or output required.

Share and Publish

R Notebooks are easy to share with collaborators. Because they’re plain-text files, they work well with version control systems like Git. Your collaborators don’t even need RStudio to edit them, since notebooks can be rendered in the R console using the open source rmarkdown package.

Rendered notebooks can be previewed right inside RStudio:

While the notebook preview looks similar to a rendered R Markdown document, the notebook preview does not execute any of your R code chunks; it simply shows you a rendered copy of the markdown in your document along with the most recent chunk output. Because it’s very fast to generate this preview (again, no R code is executed), it’s generated every time you save the R Markdown document.

The generated HTML file has the special extension .nb.html. It is self-contained, free of dependencies, and can be viewed locally or published to any static web hosting service.

R Markdown Jupyter Notebook

It also includes a bundled copy of the R Markdown source file, so it can be seamlessly opened in RStudio to resume work on the notebook with all output intact.

Try It Out

To try out R Notebooks, you’ll need to download the latest RStudio Preview Release.

You can find documentation on notebook features on the R Notebooks page on the R Markdown website, and we’ve also published a video tutorial in our R Notebooks Webinar.

We believe the R Notebook will become a powerful new addition to your toolkit. Give it a spin and let us know what you think!