What are the best practices to organize larger Shiny applications?
I think best R practices are also applicable to Shiny.
Best R practices are discussed here: How to
I wrote Radiant. I have not heard people say bad things about the code organization (yet) but I am sure it could be better. One option would be to separate the ui and logic as Joe Cheng does in shiny-partials.
https://github.com/jcheng5/shiny-partials
Another might be to try OO programming, e.g., using R6 http://rpubs.com/wch/17459