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R Markdown – Dynamic documents, presentations and reports for R

minimaxir 10y ago
R Markdown is very powerful. That being said, I still find myself using Jupyter notebooks instead due to first-class language kernel support of non-R languages (which was not the case at Rmarkdown's launch, when Jupyter was still IPython), and GitHub integration for rendering notebooks. The dynamic aspect of Rmarkdown is done through HTMLWidgets, which also works with Jupyter notebooks too. (But not via the GitHub integration mentioned earlier.)
- nicolewhite 10y ago
  I've almost fully switched from Jupyter to RMarkdown after discovering RMarkdown supports Python. And about publishing / rendering, do you not like RPubs?
  - minimaxir 10y ago
    I saw the Python examples provided awhile ago and they looked hacky. It might be worth taking another look, though. I prefer make the notebooks portable, which I can't do if they are published on Rpubs.
  - geomark 10y ago
    As well as a number of other rather useful languages [1]. Now days I use RMarkdown even for experiments because it's nice to document my line of thinking as I write the code and get a nicely formatted output when I'm finished. [1] http://yihui.name/knitr/demo/engines/ http://yihui.name/knitr/demo/engines/
  - cttet 10y ago
    I still feel the REPL-like environment in Jupyter is more suitable for building an idea, while RMarkdown is better for publishing it.
- huac 10y ago
  Have you checked out R Markdown notebooks? http://rmarkdown.rstudio.com/r_notebooks.html http://rmarkdown.rstudio.com/r_notebooks.html
  - minimaxir 10y ago
    Huh, no I haven't. That feature seems fleshed out so I'll take a look!
    - huac 10y ago
      My understanding is that full notebook support will be released in the next version of RStudio. It's available in the daily/preview builds of Rstudio, which have been fairly stable for me over the last week. https://www.rstudio.com/products/rstudio/download/preview/ https://www.rstudio.com/products/rstudio/download/preview/
      - IndianAstronaut 10y ago
        I didn't see it in the preview images, but will the notebooks have the usual Rstudio features of dataset previews and file explorer?
        huac 10y ago
        Yeah - it's basically the same workflow as Rmarkdown documents now but with inline plotting, instead of plotting to the 'plot' window (or whatever other attached graphics devices you have).
  - IndianAstronaut 10y ago
    A couple of issues I have had is that it only suppoets the R version in the Anaconda repository and thus you have to reinstall packages. It also means you have to point directly to a CRAN repository to get packages.
    - huac 10y ago
- jcheng 10y ago
  Do HTMLWidgets really work with Jupyter? I saw there is an issue but it's still open: https://github.com/ramnathv/htmlwidgets/issues/144 https://github.com/ramnathv/htmlwidgets/issues/144 Or are you referring to ipywidgets, not literally HTMLWidgets?
  - minimaxir 10y ago
    Hmm. I know plotly did as the documentation explicitly covers that use case. But the comments in the linked issue imply it is a hack.
mistercow 10y ago
This sounds a lot like how literature coffeescript works.

R Markdown is very powerful. That being said, I still find myself using Jupyter notebooks instead due to first-class language kernel support of non-R languages (which was not the case at Rmarkdown's launch, when Jupyter was still IPython), and GitHub integration for rendering notebooks. The dynamic aspect of Rmarkdown is done through HTMLWidgets, which also works with Jupyter notebooks too. (But not via the GitHub integration mentioned earlier.)

nicolewhite 10y ago
I've almost fully switched from Jupyter to RMarkdown after discovering RMarkdown supports Python. And about publishing / rendering, do you not like RPubs?
- minimaxir 10y ago
  I saw the Python examples provided awhile ago and they looked hacky. It might be worth taking another look, though. I prefer make the notebooks portable, which I can't do if they are published on Rpubs.
- geomark 10y ago
  As well as a number of other rather useful languages [1]. Now days I use RMarkdown even for experiments because it's nice to document my line of thinking as I write the code and get a nicely formatted output when I'm finished. [1] http://yihui.name/knitr/demo/engines/ http://yihui.name/knitr/demo/engines/
- cttet 10y ago
  I still feel the REPL-like environment in Jupyter is more suitable for building an idea, while RMarkdown is better for publishing it.
huac 10y ago
Have you checked out R Markdown notebooks? http://rmarkdown.rstudio.com/r_notebooks.html http://rmarkdown.rstudio.com/r_notebooks.html
- minimaxir 10y ago
  Huh, no I haven't. That feature seems fleshed out so I'll take a look!
  - huac 10y ago
    My understanding is that full notebook support will be released in the next version of RStudio. It's available in the daily/preview builds of Rstudio, which have been fairly stable for me over the last week. https://www.rstudio.com/products/rstudio/download/preview/ https://www.rstudio.com/products/rstudio/download/preview/
    - IndianAstronaut 10y ago
      I didn't see it in the preview images, but will the notebooks have the usual Rstudio features of dataset previews and file explorer?
      - huac 10y ago
        Yeah - it's basically the same workflow as Rmarkdown documents now but with inline plotting, instead of plotting to the 'plot' window (or whatever other attached graphics devices you have).
- IndianAstronaut 10y ago
  A couple of issues I have had is that it only suppoets the R version in the Anaconda repository and thus you have to reinstall packages. It also means you have to point directly to a CRAN repository to get packages.
  - huac 10y ago
jcheng 10y ago
Do HTMLWidgets really work with Jupyter? I saw there is an issue but it's still open: https://github.com/ramnathv/htmlwidgets/issues/144 https://github.com/ramnathv/htmlwidgets/issues/144 Or are you referring to ipywidgets, not literally HTMLWidgets?
- minimaxir 10y ago
  Hmm. I know plotly did as the documentation explicitly covers that use case. But the comments in the linked issue imply it is a hack.

mistercow 10y ago

This sounds a lot like how literature coffeescript works.