Okay, here is another attempt I've made. For now, this is purely done in LaTeX, but if this looks correct to you, it can be turned into a TeX template for R Markdown.
Using biblatex you can declare bibliographic categories and add entries to each category. In the end, you can print them separately as reference pages
Here is the TeX code:.
\documentclass{article}
\usepackage[style=authoryear]{biblatex}
\addbibresource{/Users/Matt/Desktop/refs.bib}
\DeclareBibliographyCategory{R}
\addtocategory{R}{R-ggplot2}
\DeclareBibliographyCategory{domain}
\addtocategory{domain}{eddelbuettel2011rcpp}
\begin{document}
Here is a great sentence about plotting (\cite{R-ggplot2}), which also has some domain content (\cite{eddelbuettel2011rcpp}).
\section*{Domain References}
\printbibliography[category=domain,heading=none]
\section*{R References}
\printbibliography[category=R,heading=none]
\end{document}
I rendered this by running, in order:
pdflatex filename
biber filename
pdflatex filename
It produces this: filename.pdf (60.8 KB)