Changed some stuff about factors and making graphs with missing factor levels.
Fixed geom_edgeset when passing only colors and not size.
Fixed geom_edgeset when passing only colors and not size.
Merge branch 'master' of https://github.com/dyerlab/popgraph

Conflicts:
	R/geom_edgeset.R
Changed theme_empty() to allow the showing of a legend IF there is a need for a legend (like using gradients for edge weights).
Made geom_edgeset order the edges from smallest to largest for plotting (so darker colors are plot over the top of lighter ones).
Changed labeling in geom_edgeset so legend is properly labeled.
Added bootstrap_popgraph function, haven't tested it yet.
cleaning up debugging of geom_edgeset
Removed the bootstrap stuff since adding a whole bootstrap_popgraph() function.
Working on finalizing options for 1.4 release.
Added labeling to edgesets via geom_edgelabel(), decorate_graph() has edge decoration, and did permute_graph() to get confidence in edge support by bootstrapping individuals within stratum.
cleaning up for clean check(as.cran) for 1.4.  This should be the final version for publication.
Change in doxygen led to changes in all man files.
made new branch for gh-pages