Hi there,
The RMarkdown output is based on LaTeX, and the default LaTeX font is Computer Modern. You will need to download and install the font on your computer. The CMU Serif version of this font is probably the one you want.
To use it in ggplot2, you may find this R Cookbook page helpful, or you can check out the extrafonts
- I've never used it but it seems like it may suit your needs.
Hope this helps!