Internal links in rmarkdown don't work

Question

I use rmarkdown to render pdf documents. Now I want to add internal links in the texts.

In the helping pages of rmarkdown, it says an internal link is defined as:

Answer 1

@rPirate has a good list, but it was missing a case that was befuddling me. I had a section header like ### 1.1.1 My Section Title that needs to be #my-section-title in the link.

After some searching, I found an official list of transformation rules in the Pandoc manual:

The default algorithm used to derive the identifier from the header text is:

• Remove all formatting, links, etc.
• Remove all footnotes.
• Remove all non-alphanumeric characters, except underscores, hyphens, and periods.
• Replace all spaces and newlines with hyphens.
• Convert all alphabetic characters to lowercase.
• Remove everything up to the first letter (identifiers may not begin with a number or punctuation mark).
• If nothing is left after this, use the identifier section.

Thus, for example,

Header                      | Identifier
--------------------------------------------------------
Header identifiers in HTML  | header-identifiers-in-html
Maître d'hôtel              | maître-dhôtel
*Dogs*?--in *my* house?     | dogs--in-my-house
[HTML], [S5], or [RTF]?     | html-s5-or-rtf
3. Applications             | applications
33                          | section