Fix remainder of r cmd check issues

This pull requests address three concerns that came up during r cmd check:

1. Non-portable filename for vignette (i.e. spaces in file path)
2. Method arguments for `plot.sla` did not match the generic arguments (for `plot`)
3. Inconsistencies and duplications in documentation (see files changed for details)

**Note to @wgalvord: GitHub comments use Markdown syntax, so you can use backticks to denote code, asterisks to denote bold and italic, etc.**