• Turning your PhD into an R Package with Bookdown examples
• Computational Resources: Hardware, Software & Training
• Mathematical typesetting (LaTeX) and reference management
• Louis Aslett: "Taming the inner loop" slides 

Further reading on optimization and computer architecture:

1. Inside the Machine by Stokes — very accessible and doesn't go into crazy details
2. Computer Architecture: A Quantitative Approach by Hennessy & Patterson (5th ed) — the Bible, even recommended internally by Intel
3. Agner Fog's work on assembly and optimization

• Literate Programming in R Markdown (slides ; source files )
• Statistical computing on CSC clusters (slides )
• How to Become a Power Linux User (slides ; more on bash scripting)