Comments (1)
See here for point choosing / fitting: https://github.com/matsen/pplacer/blob/294-likelihood-fit/lcfit_src/lcfit.ml#L138-L281
I was just evaluating the likelihood on an evenly spaced grid and dropping low-likelihood areas.
Points chosen to to evaluate impacts lcfit on a single branch quite a lot.
Choosing a grid of points for the three parameter version was also seemed difficult.
My simulations are on stoat in /loc/ssd/cmccoy/lcfit-validation
We got decent estimates of marginal probability, but (relatively) small errors led to wildly different posterior probabilities:
Rejection sampling in sts
might be better.
from sts.
Related Issues (20)
- Verify log likelihoods of trees sampled from sts HOT 4
- post-processing tool
- particles with incomplete trees HOT 1
- least-squares fitting of JC likelihood function HOT 1
- make terminology consistent
- simulations to help understand how good the "natural extension" is HOT 6
- check out performance of SMC on mixture distributions HOT 6
- inference ll != test ll HOT 3
- propose nodes to merge non-uniformly HOT 19
- A general system to store particle metadata HOT 11
- Evaluate semantics of state modifications HOT 6
- MCMC move diagnostics/logging HOT 1
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- Use lcfit for attachment branch length proposals? HOT 2
- Online: cache likelihoods
- BEAGLE has moved to version 2, whereas we are using hmsbeagle-1. HOT 1
- Propose attachment uniformly over tree length, rather than uniformly over edges HOT 1
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from sts.