Incorporate prototype-topology package

[Jason Vander Heiden]

It's probably about time to move the tree topology analysis code into alakazam, either in v0.2.1 or v0.2.2.

[Jason Vander Heiden]

Started on this. Major things that need doing:

1. Update to igraph >= 1.0 function names and arguments.
2. Swap all plyr and reshape2 code for dplyr and tidyr code.
3. Remove all non-standard evaluation.
4. Flesh out docs and examples.
5. Write a vignette.
6. Tests and testing.

[Jason Vander Heiden]

Finished item 1 (igraph>=1.0 update). I think.

[Jason Vander Heiden]

1-4 are done. We could probably replace the ExampleTree data with a more interesting set, but it's not critical.

[Jason Vander Heiden]

Replaced the example trees.

[Jason Vander Heiden]

Finished, including vignette, in bbd1d0a.