goodenuffR package: getting started with R projects
Beginners: RStudio Education: great for learning RStudio and best practices.
YAML: check out the ymlthis package for tools and documentation for working with YAML
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