Compute some transition matrix terms in log-space

Hey @mjhubisz, here is a small pull request for your changes to calculate some transition terms in log-space.  Overall, this looks good and all tests continue pass.  I just have a few comments, which I wanted to share.
I have a [logadd](https://github.com/mdrasmus/argweaver/blob/master/src/common.h#L157) for adding in log-space, which seems like what you are doing here. We could just use that, since it also uses the optimized `log1p` function.  Math checks out either way.