# Personal RMarkdown 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’s absolutely right!

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>


Check the full HTML output to see how it works. Themes can override the intended output.

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.

• the toggle word for toc is yes and not true in RMarkdown

### 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

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].

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
preserve_yaml: true