Using tikz graphdrawing library within RMarkdown …

I have the following code in an rmd file which leverages tikz for diagrams:

---
title: "TestNonTufteLua"
author: "Me"
output:
  pdf_document :
    latex_engine: lualatex
---

Prove tikz works:
```{r tikTest1, engine = "tikz"}
\usetikzlibrary{shapes}
\begin{tikzpicture}
    \node[ellipse, draw=black, align = center] (Data) {Data $y_{n}$};
\end{tikzpicture}
```

Then, when you set `eval = TRUE` in the below code, it will not work. 
```{r tikTest2, eval = FALSE, engine = "tikz"}
\usetikzlibrary{graphs, graphdrawing}
\usegdlibrary{layered}
\tikz [gr/.style={gray!50}, font=\bfseries]
\graph [layered layout] {
    % A and F are horizontally aligned if you also set weight=0.5 for A -- C.
    A -- [minimum layers=2] C -- F,
    { [nodes=gr, edges=gr] A -- B -- { E, D -- F } }
};
```

When changing to eval=TRUE in the second chunk, I get the following error:

Quitting from lines 24-29 (testNonTufteLua.Rmd) Error: running 'texi2dvi' on '.\tikz36747a021b22.tex' failed

LaTeX errors: rarygraphdrawing.code.tex:22: Package pgf Error: You need to run LuaTeX to use the graph drawing library.

This error occurs when using the knit button from RStudio or using render("testNonTufteLua.Rmd", output_format = pdf_document(keep_tex = TRUE, latex_engine = "lualatex"). I have also experimented with setting options(tikzDefaultEngine = "luatex") to get tikzDevice to handle it properly, but it still does not work. I just can't seem to get the graphdrawing library to work even though the tikz-shapes library can be loaded and also that the rest of the document seems to be compiled with lualatex. Thanks for any help!!

This is rather tricky, since you are not using tikzDevice but the tikz engine, which uses tools::texi2dvi to convert to PDF. You can change this using options(texi2dvi = "lualatex"). However, the default template does not work with LuaLaTeX. I have therefore created a modified template:

\RequirePackage{luatex85}
\documentclass{article}
\usepackage[luatex,active,tightpage]{preview}
\usepackage{amsmath}
\usepackage{tikz}
\usetikzlibrary{matrix}
\begin{document}
\begin{preview}
%% TIKZ_CODE %%
\end{preview}
\end{document}

And specify that file with engine.opts = list(template = "tikz2pdf.tex"). Putting it all together here my working file:

---
title: "TestNonTufteLua"
author: "Me"
output:
  pdf_document :
    latex_engine: lualatex
---

```{r}
options(texi2dvi = "lualatex")
```

```{r tikTest2, eval = TRUE, engine = "tikz", engine.opts = list(template = "tikz2pdf.tex")}
\usetikzlibrary{graphs, graphdrawing}
\usegdlibrary{layered}
\tikz [gr/.style={gray!50}, font=\bfseries]
\graph [layered layout] {
    % A and F are horizontally aligned if you also set weight=0.5 for A -- C.
    A -- [minimum layers=2] C -- F,
    { [nodes=gr, edges=gr] A -- B -- { E, D -- F } }
};
```

Result: