I'm generating static HTML pages using Rmarkdown for a large set of users. Each gets their own HTML output. The end users have variable IT savvy. I generate new HTML files every two weeks for each client, but also keep historical files as well. Right now I am using WordPress to display the current HTML file (within iframe), and have a clumsy file picker on the side. But it just feels like the wrong tool. Given how many users are generating regular reports with markdown/knitr, this must be a solved problem. I'd love to know what others are doing.
RMarkdown may well be the right tool to use to generate your HTML reports. It's ideal as a template for generating fresh reports when new data comes in.
Your question however seems to be more about the design of the user interface for a website where users can download (or even generate) their reports. This I think is more of a general web design question, it's not really about R. You might even be able to solve your problem by providing a shared folders for each user via a service like Dropbox.
RMarkdown can be programmed to export its knitted output to a particular folder depending on variables such as user ID, or anything else.
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