What happens if you ask for too much power from Markdown?
R Markdown is one of the document formats that knitr supports, and it is probably the most popular one. I have been asked many times about the choice between Markdown and LaTeX, so I think I'd better wrap up my opinions in a blog post. These two languages (do you really call Markdown a language?) are kind of at the two extremes: Markdown is super easy to learn and type, but it is primarily targeted at HTML pages, and you do not have fine control over typesetting ( really? really?), because you only have a very limited number of HTML tags in the output; LaTeX is relatively difficult to learn and type, but it allows you to do precise typesetting (you have control over anything, and that is probably why a lot of time can be wasted).
What is the problem?
What is the root problem? I think one word answers everything: page! Why do we need pages? Printing is the answer.
In my eyes, the biggest challenge for typesetting is to arrange elements properly with the restriction of pages. This restriction seems trivial, but it is really the root of all "evil". Without having to put things on pages, life can be much easier in writing.
What is the root of this root problem in LaTeX? One concept: floating environments. If everything comes in a strictly linear fashion, writing will be just writing; typesetting should be no big deal. Because a graph cannot be broken over two pages, it is hard to find a place to put it. By default, it can float to unexpected places. The same problem can happen to tables (see the end of a previous post). You may have to add or delete some words to make sure they float to proper places. That is endless trouble in LaTeX.
There is no such a problem in HTML/Markdown, because there is no page. You just keep writing, and everything appears linearly.
Can I have both HTML and PDF output?
There is no fault being greedy, and it is natural to ask the question whether one can have both HTML and PDF output from a single source document. The answer is maybe yes: you can go from LaTeX to HTML, or from Markdown to LaTeX/PDF.
But remember, Markdown was designed for HTML, and LaTeX was for PDF and related output formats. If you ask for more power from either language, the result is not likely be ideal, otherwise one of them must die.
How to make the decision?
If your writing does not involve complicated typesetting and primarily consists of text (especially no floating environments), go with Markdown. I cannot think of a reason why you must use LaTeX to write a novel. See Hadley's new book Advanced R programming for an excellent example of Markdown + knitr + other tools: the typesetting elements in this book are very simple -- section headers, paragraphs, and code/output. That is pretty much it. Eventually it should be relatively easy to convert those Markdown files to LaTeX via Pandoc, and publish a PDF using the LaTeX class from Chapman & Hall.
For the rest of you, what I'd recommend is to think early and make a decision in the beginning; avoid having both HTML and PDF in mind. Ask yourself only one question: must I print the results nicely on paper? If the answer is yes, go with LaTeX; otherwise just choose whatever makes you comfortable. The book Text Analysis with R authored by Matthew Jockers is an example of LaTeX + knitr. Matt also asked me this question about Markdown vs LaTeX last week while he was here at Iowa State. For this particular book, I think Markdown is probably OK, although I'm not quite sure about a few environments in the book, such as the chapter abstracts.
It is not obvious whether we must print certain things. I think we are just too used to printing. For example, dear professors, must we print our homework? (apparently Jenny does not think so; I saw her grade homework on RPubs.com!) Or dear customers, must we submit reports in PDF? ... In this era, you have laptops, iPad, Kindle, tablets and all kinds of electronic devices that can show rich media, why must you print everything (in black and white)?
For those who are still reading this post, let me finish with a side story: Matt, a LaTeX novice, taught himself LaTeX a few months ago, and he has finished the draft of a book with LaTeX! Why are you still hesitating about the choice of tools? Shouldn't you just go ahead and get the * done? Although all roads lead to Rome, some people die at the starting line instead of on the roads.