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:

See the [Introduction](#introduction).

When I Use e.g. the next code there should be two internal links: link1 and link2. Both don't link. Is there something obvious that I am doing wrong? Many thanks in advance!

   ---
title: "Test"
author: "test test"
output:
  pdf_document:
    latex_engine: xelatex
    number_sections: yes
    toc: yes
    toc_depth: 3
  html_document:
    css: tables.css
    number_sections: yes
    theme: cerulean
    toc: yes
    toc_depth: 3
subtitle: test test test
mainfont: Calibri Light
fontsize: 12pt
header-includes:
- \usepackage[dutch]{babel}
- \usepackage{fancyhdr}
- \pagestyle{fancy}
- \fancyfoot[LE,RO]{this is a fancy foot}
- \usepackage{dcolumn}
- \usepackage{here}
- \usepackage{longtable}
- \usepackage{caption}
- \captionsetup{skip=2pt,labelsep=space,justification=justified,singlelinecheck=off}
---

# start

```{r results="asis",tidy=FALSE,eval=TRUE,echo=FALSE,message=FALSE, error=FALSE, warning=FALSE, comment = NA}
cat("click here: [link1](#test 1)")
```

click here: [link2](#test 1)

\pagebreak

#test 3

\pagebreak

#test 2

\pagebreak

#test 1

Solution 1

You're not setting the anchors correctly.

Try the following:

# start

```{r results="asis",tidy=FALSE,eval=TRUE}
cat("click here: [link1](#test1)")
```

click here: [link2](#test1)

\pagebreak

# test 3 {#test3}

\pagebreak

#test 2 {#test2}

\pagebreak

#test 1 {#test1}

Solution 2

There are some tricky rules for internal links in Rmarkdown PDF output, not well documented on cheat sheets, etc.

Rules:

• Only one # for anchor, even if you are using a header with multiple #.

  Example: ###header becomes #header when linking.

• No spaces between # and anchor text.

  Example: #header, not # header.

• Multi-word anchors should be separated by dashes.

  Example: #this is a header needs to become #this-is-a-header in the link.

• Anchor links need to be lowercase, even if the header you are linking to has capitalization.

  Example: #Section becomes #section in the link.

Solution 3

@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

Solution 4

Josh Paulson has an article on Rstudio website that goes into details. Here is his solution

Slide 1
====================================
id: slide1

Slide 2
====================================
[Go to slide 1](#/slide1)

This works me. A Handcart And Mohair's code does not work on RHTML

Solution 5

Here is a simple way of doing internal links/references in an RMarkdown PDF document:

A) Create a section header:

## Homework Assignments{#hwks}

B) After creating the section header. I can refer to it in my text like this:

If you are having a hard time with your [homework](#hwks), we have some tutors who can help you. 

This creates a link back to the section header entitled "Homework Assignments".

Notice a couple of things in the way I set up the link:

1. "homework" ==> the word (or phrase) I use to call the header is in brackets

2. [homework] is immediately followed by the identifier "#hwks" that I created above, but the identifier is now in parentheses, as in: (#hwks)

This always works for me!

(This was my first post here; I hope it makes sense. :) )

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