Personal Markdown Resources

To paraphrase Prof Alex Slocum¹², if you are a serious researcher in this century, you should have a website; and if you don’t, don’t expect to talk.

I believe that he is absolutely true! I use markdown extensively to write everything from emails to technical documents and manuscripts.

These are shortcuts/ tricks/ resources that I’ve looked up over time. Just posting it here for future reference- yours and mine.

1 To change fonts inline in Markdown

<p class=text-center style="font-family: Georgia, serif; font-size:11pt; font-weight:bold">
 This is how you do it!
</p>

gives

This is how you do it!

General styling tweaks are discussed in Section: Text formatting and Styles

1.1 Useful list of Fonts

• Arial (sans-serif)
• Verdana (sans-serif)
• Helvetica (sans-serif)
• Tahoma (sans-serif)
• Trebuchet MS (sans-serif)
• Times New Roman (serif)
• Georgia (serif)
• Garamond (serif)
• Courier New (monospace)
• Brush Script MT (cursive)

As you can see, this is not the most elegant solution for inline changes in text formatting. If it were so, I would have converted each of the above list entries to the fonts they represent.

2 Toc - Table of Contents

• the toggle word for toc is yes and not true

2.1 Indentation

• the following script will take care of indentation in the toc list:

<script>
$(document).ready(function() {
  $items = $('div#TOC li');
  $items.each(function(idx) {
    num_ul = $(this).parentsUntil('#TOC').length;
    $(this).css({'text-indent': num_ul * 10, 'padding-left': 0});
  });

});
</script>

• Use number_sections: true in the header for numbering. Levels are intuitively expressed using decimal dots and are equivalent to the number of # signs prefixing the heading. But to display more levels than the default 3 (H3) levels, use toc_depth: 5 in the header.

2.2 TOC anywhere on the page

• This can be done (as I have chosen to do for this article) by making use of Shortcodes. Checkout the details and implementation in Ref. 4

3 Text alignment

• While its possible to use css to do this, I often use the following html snip for flexibility

<div class=text-justify>
body
</div>

4 Text formatting and Styles

• the following snippet of code can be placed in the markdown body as a work around to text styling.

<style type="text/css">

body{ /* Normal  */
      font-size: 12px;
  }
td {  /* Table  */
  font-size: 8px;
}
h1.title {
  font-size: 38px;
  color: DarkRed;
}
h1 { /* Header 1 */
  font-size: 28px;
  color: DarkBlue;
}
h2 { /* Header 2 */
    font-size: 22px;
  color: DarkBlue;
}
h3 { /* Header 3 */
  font-size: 18px;
  font-family: "Times New Roman", Times, serif;
  color: DarkBlue;
}

</style>

4.1 Themes

The list of themes available to call from the header via theme is available at Bootswatch³

5 Internal Links

I have used an implicit link in section To change fonts inline in Markdown.

The syntax is to use the correct heading you want to link to within square brackets:

I have used an implicit link in section [To change fonts inline in Markdown].

6 Footnotes

The syntax is as follows. Scroll down to see how they appear.

Footnote 1 link[^first].

Footnote 2 link[^second].

Inline footnote^[Text of inline footnote] definition.

Duplicated footnote reference[^second].

[^first]: Footnote **can have markup**

    and multiple paragraphs.

[^second]: Footnote text.

7 Converting to GFM

The front matter specifics:

output:
  md_document:
    variant: gfm
    toc: yes
    toc_depth: 5
    number_sections: true

8 Reference

1. markdown-it
2. R Markdown: The Definitive Guide
3. Reproducible Templates for Analysis and Dissemination Course by Emory University
4. Table of Contents Shortcode

---

1. Tea with Alexander Slocum: an interview↩︎

2. Alex Slocum’s website↩︎

3. Rmarkdown Catalogue↩︎