simmap now uses meta nodes instead of raw XML, passes test_simmap.R
Includes implementation mapping phy tip states to character matrix.
Also implements substitutions of state values for state ids when generating the character matrix.
Doesn't handle the case of making character node and ids when no phy is available.
(Perhaps phy can just be generated from the edge mappings in that case?)

Also, doesn't include the simmap:char meta element indicating which character is being used. must be added
give file as second argument.
since trees and characters arguments are more natural to always give as named arguments, while
other R functions often omit file and follow the convention of having it as the second argument
simmap states order explicitly now
added travis file
updated name and organization
update documentation
merge
update documentation
re-organize vignettes
updating documentation
working on check
add additional suggests packages for testing and extensions
update documentation
update README