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ArtPoon / kamphir

Phylogenetic inference using a tree-shape kernel in an Approximate Bayesian Computation framework
BSD 3-Clause "New" or "Revised" License
6 stars 2 forks source link

Getting negative values for coalescent dot-product kernel #44

Closed ArtPoon closed 9 years ago

rmcclosk commented 9 years ago

That's only possible if some of the node heights are negative. I didn't realize that could happen. Probably the fastest thing to do is just square it.

ArtPoon commented 9 years ago

I'm going to shift the origin if there are negative node heights

On Jul 21, 2015, at 4:03 PM, Rosemary McCloskey notifications@github.com wrote:

That's only possible if some of the node heights are negative. I didn't realize that could happen. Probably the fastest thing to do is just square it.

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rmcclosk commented 9 years ago

Sorry I didn't consider this. FWIW it doesn't actually make sense to get negative node heights out of colgem if you start the epidemic at time 0. Because then those node heights are before the epidemic started...