Technical review of R Markdown PDF report

[riccardoporreca]

The R Markdown PDF report should be cleaned-up, so that it is technically cleaner.

Examples:

• Review / cleanup LaTeX code in header.tex and the main report
• library(...) statements at the beginning
• HTML-releated statements like <br>
• general code organization review

We probably also want to switch away from leaving metadata like title and author in the YAML header and using a customized first page, which means the PDF output does not have such properties. An option for this is to switch to a custom Pandoc template, which would be a nice maintenance refactoring, especially if we want to customize the appearance of the report in the future.