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.

[riccardoporreca]

Details to be discussed, see premature PR #138 (review) comment.

[RolandASc]

Maybe update (replace) the link to .../apps/smarp at the same time

[gabrielfoix]

Ready to start.
Roland's comment will be addressed in another issue together with similar updates.
Talk to @riccardoporreca to define scope and approach.

[riccardoporreca]

Maybe update (replace) the link to .../apps/smarp at the same time

Covered by #143

[riccardoporreca]

Note that, in general, we shall reconsider if we want to keep using xelatex as engine, as well as whether PDF version (vector graphics) of the figures can be created and used instead of PNG.

Originally posted by @riccardoporreca in #152 (comment)