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A few more thoughts from @markeschaffer (moved from issue #11)...
The structure of the model is in terms of proportions of adults rather than proportions of children, which makes sense. But it make…
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It appears as though SpeciationCV and VariableCV are being confused in the validation step:
 setMeanBranchExtinction and setMeanBranchSpeciation are called all over the place. They were useful when we were outputting branch-specific speciation…
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If `a == b` then also should be `beast.math.MachineAccuracy.same(a, b) == true`. However, this fails when `a = b = 0.0` because `a / b` evaluates to not-a-number.
Proposed fix (using an idea suggeste…
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Early on I remember we discussed the naming of parameters in the bammdata object. I agreed to use $lambda for beta (for trait evolution) for simplicity. However, this is definitely going to confuse pe…
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couple of suggestions-
1) for plot.bammdata, there are lots of not-great color schemes and some awesome ones, just because this fxn has lots of flexibility. I suggest explicitly detailing a set of "…
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R functions for summarizing rates etc for speciationextinction model but I don't think they are yet finished for trait evolution.