Revert "Moving \SweaveOpts to after \begin{document}"

This reverts commit 6f2cfbb2a948fa5350b72ba79275cc38da5b8fae.
Show missing plots

Figures 10 and 14 had captions but no plots.
Also fixed an equation reference and a couple of typos.
Merge pull request #1 from gustavdelius/Updated-vignette

Fixing some typos in the vignette
Fixed predation mortality equation
Tried to fix cross machine problem with remainder check
Merge pull request #4 from gustavdelius/Updated-vignette

Show missing plots in vignette
Finlay's fix for remainder check