merge a few edits

See merge request !3

Re run ellis full data

See merge request ba1e12/datacleaning!4

Re run ellis full data

See merge request ba1e12/datacleaning!3

Re-run ellis full data

See merge request ba1e12/datacleaning!2

added reporting of duplicates; trying to fix tables for pdf output. Vanilla kableExtra::kable() should do it?

Re run ellis full data

See merge request ba1e12/datacleaning!1

> install.packages(c('tinytex', 'rmarkdown'))
> tinytex::install_tinytex()

#rtfm

amended to enable a way to force report update; pdf still fails, unclear why; render is still ignoring floating ToC. Have seen this before, can't remember the cause/fix

fixed bib (was absent); html no longer self-contained so plots exist seperately; floating ToC still broken in html (why?); pdf fails (probabky table too big)

amended to reflect slight restructure: only Rmd in /Rmd; drake make & plans at top level (not in /R as drake recommends); outputs into /docs