Insert a logo in upper right corner of R markdown pdf document

Ok, I have found the solution:

---
title:
header-includes: 
   \usepackage{graphicx}
   \usepackage{fancyhdr}
   \pagestyle{fancy}
   \setlength\headheight{28pt}
   \fancyhead[L]{\includegraphics[width=5cm]{GPIM_Logo_300x85.png}}
   \fancyfoot[LE,RO]{GPIM}
output: pdf_document
---

You can use the includes option in the yaml to specify a custom addition to your latex header. The yaml part would look like

---
output: 
    pdf_document:
      keep_tex: true
      includes:
          in_header: header.tex
---

and you need to save a separate file called header.tex with the following defining your company logo like so:

\usepackage{fancyhdr}
\pagestyle{fancy}
\rhead{\includegraphics[width = .05\textwidth]{logo.png}}

Here I used the fancyhdr latex package to add the logo, but there are other potential solutions. See here for more options.