Myriad fixes, edits and additions

This PR includes a thorough edit for consistency, typos etc. plus the following substantive additions

 * fiddled with the figures, esp the stratigraphic plot to give it more height
 * figures now generated as TIFF and EPS (`postscript()`) as well as PNG as those formats are better for journal submissions
 * `dpi=300` used throughout as per journal reqs.
 * fixes for problems in the bibliography `.bib` file

The general edits supercede some of the changes I proposed in PRs #27 and #28 which seem to have been overlooked. We should revisit those changes if this PR is merged, as I may not have included all of them here.