Greek unicode in R Markdown

[jdlong]

I have a bookdown book with a lot of greek symbols inline. I've put them in using, I presume, Unicode. In RStudio the text looks like this example:

we get the coefficients (*β*~*i*~) 

Which is nice in that it actually shows the Greek character beta. If I render to gitbook or other HTML it looks as expected. However if I render it to LaTeX (book down::pdf_book) the beta is totally missing:

I realize I could go through and replace all my betas with $\beta$ but that's a daunting prospect given the size of the book.

I tried switching from pdfLaTeX to XeLaTeX to no avail. Any ideas on how I might make my β as well as my α and λ show up in LaTeX?

[technocrat]

Moving parts:

1. The input code
2. The options given to pandoc for conversion, via tex to pdf
3. The use of a UTF-8 font that supports the Greek and math symbols, which may have to be specified

Even in the tex file used to generate the image, there's a slight misstatement about direct Unicode. What was actually entered was ȃ ≅Ŷ, but the rendering dropped the ≅symbol.

I think you have two additional unpalatable choices in addition to the one you identified, which isn't actually that bad given that stringr handles Unicode pretty well:

1. Run your Rmd files from the command line and call knitr with your own pandoc flags, which basically means reverse engineering from a tex that outputs what you want.

2. Edit the tex files, but no one is that masochistic.

Here's the tex file I used:

% Input to XeLaTeX is full Unicode, so Unicode characters can be typed directly into the source.


\documentclass[12pt]{article}
\usepackage{fontspec}
\usepackage{graphicx}
\usepackage{amssymb}
\newfontfamily\unicodefont{Lucida Grande}

\title{Greek unicode in R Markdown}
\author{Richard Careaga}
%\date{} 

\begin{document}
\maketitle




we get the coefficients (*β*~*i*~)  raw (in your example)

we get the coefficients (\emph{β}\textsubscript{\emph{i}}) after plain pandoc conversion 

or we get  ($\beta \thicksim i$) in native tex, with XeLaTeX engine, but not pdflatexmk

Here is some direct Unicode: ȃ ≅Ŷ in the tex file

\end{document}  

Oh, one other thing. \tilde positions atop the preceding character, you need \thicksim for a standalone.

[jdlong]

@technocrat

Unicode: ȃ ≅Ŷ in the tex file

Good reproduction of the issue I'm facing. In your example do you understand why the ≅ is getting dropped?

Also, I'm perplexed as to why the unicode gets rendered properly in HTML:

[jdlong]

I copied and pasted the whole greek UTF-8 table from here into my book just for testing. All the greek characters render fine in HTML but with XeLeTeX only some of them do.

You can see in this subset (colored boxes added for emphasis) that the core uppercase greeks work fine but not the lowercase:

Interestingly, this is the case whether I surround the text with code ticks ``` or not. Even though code text uses a different font than body text.

So I decided that this must be a font issue. After re-reading a lot of the Bookdown book I realized that I can change the font by changing a few settings in my index.Rmd file. So as an experiment I added the following to my YAML:

mainfont: Arial
monofont: "Courier New"
monofontoptions: "Scale=0.7"

Future travelers should note that the above font options are ONLY applicable when using XeLaTeX... other LaTeX engines use different options to change fonts.

Then when I rendered my book to PDF all worked as expected:

So the issue was the default font used by XeLeTeX.

[technocrat]

(β~i~)

XeLaTeX is supposed to allow direct unicode entry in the source, but it depends on which source editor one uses is my best guess from multiple experimentation.