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RMarkdown output option prettydoc does not allow for toc_float which is why the Table of Contents is at the top of the page. (Source: https://prettydoc.statr.me/). In order to get a side panel table of contents, a different output option/them would need to be used.
To increase user navigability, move Table of Contents to side panels (where it's always visible) instead of at top of page
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