That is why I recommend running the PDF anyways, to make sure it is birthed properly, but still look at the output in HTML only (which will always be beautiful and make you happy). You don’t want to write your whole thesis (or even half of it) and then realize that the PDF just doesn’t compile, because you won’t solve that in just a few hours. Such issues can often be resolved by reinstalling stuff, but sometimes it’s a simple thing like some weird symbol in your table. HTML is more lenient than PDF in that it will (almost) always run and at most show you funky output in cases where \(\LaTeX\) will just crash with an error message that you will probably not understand. However, I do recommend generating the PDF output anyways, just to check that it compiles. I agree that HTML output is more reliable in terms of formatting, while \(\LaTeX\) (PDF) output can have some weird stuff that will put you off, such as ugly or not well positioned tables (that looked so good in the HTML version!) or code that runs out of the margins if you use code-snippets. Leave the job of careful typesetting to the very end (ideally after you have really finished the content of the book). We strongly recommend that you use an HTML output format instead of LaTeX when you develop a book, since you will not be too distracted by the typesetting details, which can bother you a lot if you constantly look at the PDF output of a book. However, I first focused on the HTML only because when I started looking into bookdown I found this: I knew from the beginning that I wanted at least those two formats: PDF for the printed version that I would have to hand in and HTML to show it to the world in a digital version, like all those other online books I was loving to find. I will only talk about the first two because they are the ones I used. The bookdown package supports three main formats: HTML, PDF and e-books.
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