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I'm an experienced programmer but new to R, working on a visualization project that would be months of work in D3.js (but client knows R, not JavaScript.) I may have to start from a clean slate again once I figure out what I'm doing, but at the moment, I'm just trying to decide what kind of object to start with. If I make a new R Markdown document (in RStudio), Shiny is one of my output options; or I can make a new Shiny app without markdown.

I can guess what some of the trade offs might be:

  • R Markdown might be a good playground for trying stuff, documenting it as I go along, and sharing it with clients.
  • But the quoting and embedding options add an extra layer of stuff I'm not proficient with.
  • Working on a plain Shiny app might allow me to focus more on learning Shiny, but it might tempt me to over-design the app before I know what I'm doing, and I should probably be focusing more on learning R and ggplot2 and experimenting with the data and possible Shiny widgets (which R Markdown should be good for.)

The question of what I should do is opinion-based, and I understand that's not what StackOverflow is for. But just writing out the question has helped me understand the differences between these options. So my real question is: have I understood the relationship between Shiny and R Markdown correctly or am I missing something important?

Edit. Based on clarifying questions in comments, my needs are: a good playground for learning R, exploring the data and ways of letting users interact with it, documenting these experiments, and serving as a scratchpad for components that will form a more coherent application eventually. Based on this question, R Notebook might be more appropriate for a first pass than regular R Markdown, but it doesn't have a prepackaged Shiny option, so R Markdown with Shiny is probably best for now.

Sigfried
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  • Just use normal R scripts and then use rmarkdown if you need the extensive documentation/output features? – zacdav Aug 06 '18 at 15:01
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    It is not very clear on how the final product will be used and how often it needs to be refreshed and read. A interactive web page, one long document, a presentation? – Dave2e Aug 06 '18 at 15:02
  • I'll have to try a lot of things and let the users play with them. The output will be interactive, multivariate visualizations allowing users to assign data dimensions to display characteristics and to dynamically configure aggregation and filtering. So, if it starts as shiny inside markdown, it may eventually shift to being a pure R/Shiny app, but probably with several blind alleys along the way. – Sigfried Aug 06 '18 at 17:11
  • I should have found this earlier: https://shiny.rstudio.com/articles/app-formats.html – Sigfried Aug 07 '18 at 14:13

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