The answer is to use a template file, but you need to tweak a bit for its bit:
--- title: "My report" author: "me" output: pdf_document: toc: yes includes: in_header: style.tex ---
Prepare the document "style.tex" in the same folder as your markup file, and make sure that you change the working directory in R to this folder.
Add the following lines to your style.tex file:
\institute{My institute} \pgfdeclareimage[width=2cm]{logo}{logo.png} \usebackgroundtemplate{\pgfuseimage{logo}}
Thanks: Inserting a logo into a ray presentation using R Markdown
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