Implement some of the reviewers' comments.

Some clarifications should fix #13, #14, #15, #16, #18 and #19.

Added an alternative `stateTime' figure which excludes PB1, PB2 and HA
trees to avoid confusion.

Changed `LineageRatiosOverTime' figure to include genome counts at the
top to clarify that it shows something extremely basic.

Also altered LD calculator a bit, it didn't work with time-slicing
before and now does. I was trying to animate LD over time, didn't look
as impressive as expected.