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Making Git and Jupyter Notebooks play nice

timstaley.co.uk

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Re: Making Git and Jupyter Notebooks play nice

#31

Post by clatan »

wodenokoto wrote: post #28

A lot of people mentioning what is essentially R markdown files as a better approach. In .rmd the notebook is just markdown where code segments inside triple backticks can be executed. That sounds nice and git compatible (and it is), but you lose a lot of the convenience of Jupiter notebook, namely that output isn’t stored together with input. The nice thing about Jupyter notebooks is you get story, code and results…

the .rmd is just text. But the output is cached separately, RStudio can load the full notebook, code and output. So it seems to me it's only a matter of how to integrate the .rmd with the output data so it can be displayed in interfaces other than RStudio.

Plus you get the option of rendering an HTML which IMO is no different than having a jupyter file.

Re: Making Git and Jupyter Notebooks play nice

#32

Post by bobongo »

wodenokoto wrote: post #28

A lot of people mentioning what is essentially R markdown files as a better approach. In .rmd the notebook is just markdown where code segments inside triple backticks can be executed. That sounds nice and git compatible (and it is), but you lose a lot of the convenience of Jupiter notebook, namely that output isn’t stored together with input. The nice thing about Jupyter notebooks is you get story, code and results…

At the beginning of your Rmd file, add a chunk that spins your Rmd file to an R script.

https://www.garrickadenbuie.com/blog/convert-r-markdown-rmd-...

Now you have:

- single file (Rmd, plain text) where you can do any edits, which, when compiled, produces:

- (1) you get story, code and results in a single package: one output file (usually, html), where all inputs and outputs are stored together (or, just the outputs, if you turn off echo'ing, e.g. for producing a report),

- (2) you get the code: another output file, which is a simple R script version of your Rmd file.

Code updates to the Rmd are viewable much easier on the output R script (#2), which is also much more convenient for debugging. For static text updates, I look at the Rmd file. For content updates (e.g. did my data change between the runs?), I look at the html (or Word or PDF etc) file (#1).

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