hi comandra,
i’m also working in environmental science and also depend heavily on R for data analysis. i dug into the whole obsidian/zettelkasten universe earlier this year only.
i was wondering when reading your question about the file-links - are you separating your rstudio projects and your obsidian vault?
at the moment i’m doing so, but as the vault also contains information related to the project that the RStudio-Analysis is based in, I’m noticing more and more that the division of information of those two is not helpful for keeping the overview. my compromise at the moment looks like this: (semi-automatically) synchronizing my Rstudio-“Results/Plot”-folder to the Obisidian vault to make it possible to embed plots in notes with the proper file path.