Run lintr over the project and amend code presentation accordingly

[francisbarton]

1. Issue addressed by this pull-request: Internal: Run lintr over the project and amend code presentation accordingly #125

2. Changes proposed in this PR:

• Mainly just various presentational/formatting changes such as line length to comply with tidyverse code style, indentation of brackets, inline functions wrapped in {} where covering more than 1 line
• Also some changes to, for example, quote variables, wrapped in pick() or if_any() etc.
• Small amount of unnecessary code removed and some lines simplified
• # nolint comment used where line lengths cannot currently be further shortened or to avoid object not used warnings from lintr (several R objects are created in order to be referred to in the report .Rmd file, but are not further referred to within the current R function)
• Removes unnecessary use of all_of() to wrap named column names - these were introduced by me in the first place :-/

3. People who will review this PR: @ThomUK

Please confirm that you have:

• Run devtools::test() and fixed all failing tests and warnings.
• Added suppressMessages() to any test message which breaks the test progress UI.

R CMD check also passes. Documentation (.Rd files) has been regenerated.

Version bumped in DESCRIPTION.