Setting \rho without tip labels in tree.kernel() generates strange outputs

PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference

GNU Affero General Public License v3.0

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Setting \rho without tip labels in tree.kernel() generates strange outputs #136

Open ArtPoon opened 6 years ago

ArtPoon commented 6 years ago

\rho is supposed to control whether the kernel matches exclusively subtrees (all the way to the tips) or subset trees. Setting rho=0 should result in a subtree kernel. The resulting scores are failing normalization --- sqrt(k(t1,t1) * k(t2,t2)) is less than k(t1,t1).

ArtPoon commented 5 years ago

Re-implemented tree kernel in R - see if this still happens