Most publications I work with frown on graph titles in preference to captions. If you use Rmarkdown with the bookdown package you can build documents that embed your graphs with captions that you can cross reference in your text. Despite the title, it is great for papers as well as books. https://bookdown.org/home/. Source: over 2 years ago
It’s just that you need to run a Linux server to host a shiny app. You can’t complete to a webpage. But you can use BookDown. https://bookdown.org/home/. Source: over 2 years ago
Just an fyi that these are not mutually exclusive. You can use a custom latex template for the pandoc pdf translation while still using rmarkdown for your actual writing. Details here. Also, for something dissertation length you might want to look into the bookdown package; related. Source: over 2 years ago
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