Document custom ordination process

We have all the components (rarefaction, consolidation at family level, `prcomp` calls to get loadings, etc) needed to make a nice little helper function that does all the work, but those are also the steps that a user may want to do differently for their ordination. We don't have to come up with every possible parameter ahead of time for a helper function if we just provide an example script highlighting areas someone may want to tweak.

Start by locating the existing rarefaction, family-level consolidation, and prcomp calls in the R package, then review any current examples or documentation. Add an example script showing the ordination workflow and the steps users may want to modify; done means the script is understandable and reproducible.

Written by the indexing model from the issue text.