Extra attributes in simulate.binary.dated.tree.fgy output uses a lot of space

[gtng92]

(From issue #42) I got the function run.smc to work for sir.nondynamic model with changing the parameters in pkg/examples/example-compartmental.yaml ...but only for nparticle=3. Any higher with my current parameters, it breaks again with the "negative probability error". I'll continue changing the parameters some more, but there's something else that I've noticed.

With the resolved casting of an rcolgem simulate.binary.dated.tree.fgy object to a phylo object (issue #79), the 5 attributes required of a phylo object are stored into a given simulated tree, but an additional 20 attributes from the rcolgem simulate.binary.dated.tree.fgy object remains as part of the object.
This isn't an issue for a single simulated tree, but I noticed that when I run.smc on 3 particles, one step/iteration takes about 9.8 seconds, and the result is a large list of 2 elements, 1.1 Mb.

Should the additional attributes be removed?

[ArtPoon]

I would say yes. Please determine which member variables correspond to phylo object variables and which do not (are rcolgem specific) and remove, when returned from rcolgem.