YAML: check out the ymlthis package for tools and documentation for working with YAML
Markdown: Commonmark has a quick ten-twenty minute tutorial on markdown.
R Markdown: A comprehensive but friendly introduction to R Markdown and friends. Free online!
R for Data Science: A comprehensive but friendly introduction to the tidyverse. Free online.
R Markdown for Scientists: R Markdown for Scientists workshop material
The ggplot2 book
ggplot2 on the tidyverse website