Hi Alex,
I think that, given that the report will be just chunks of info generated incrementally every day or so, instead of writing a whole .Rmd file perhaps you can use knitr::spin to generate the output from an .R script. You can find more info on this post: deanattali.com/2015/03/24/knitrs-best-hidden-gem-…
On the other hand, take a look at knitr's cache option: yihui.name/knitr/options which allows you to save the result of computed chunks and avoiding the re-execution every time you knit the document. The downside of this approach is that you have to be very careful about what things are cached or not, because it can cascade out-of-date results to other chunks along the way. Please handle with care!
Hope this helps.