Fix typos, dead links, outdated information across various chapters

[engineerchange]

Various changes throughout the repo. These include:

• typos (e.g., "randon" -> "random", "idenfity" -> "identify", "generall" -> "general", etc.)
• typos with markdown (e.g., missing the ` character)
• dead links (e.g., AMD has different libraries now, EPA dataset website has changed, bell-labs url is dead)
• code not repeatable (e.g., readLines() with jhsph.edu has significantly different (longer) output now, changed code block to use en.wikipedia.org)
• outdated information (e.g., stringsAsFactors doesn't default as TRUE, but now defaults as FALSE)

Notes:

• The repo doesn't have instructions on how to develop and submit PRs, so I only changed the .Rmd files.
  • Transforming from '.Rmd' to '.md' changes some of the code output, perhaps inappropriately, as random seeds are not set in the first half of the book. Also, in the 'parallel' chapter, the computation is dependent on a specific type of laptop. I leave this last step of converting to .md and subsequent generation to bookdown format to the maintainers.

Please let me know of any edits required by maintainers.