Closed GoogleCodeExporter closed 9 years ago
Adding all the <upDownOperators> with only one parameter is the equivalent of
just adding extra scale operators for these parameters. This suggests the
weights of these operators should be increased by default. Need to check if the
updown interation of these parameters would also help.
Original comment by ramb...@gmail.com
on 18 Dec 2013 at 12:10
The issue is not with the "<upDownOperators> with only one parameter".
What is missing is the *combined* upDownOperator, which includes the species
tree, all gene trees and all the relevant rates (birth death, pop sizes and
gene clock rates).
Original comment by jhe...@gmail.com
on 18 Dec 2013 at 12:16
But the single-parameter operators are what the user claimed improved mixing.
It may be worth increasing the weights of these too? I think these will mostly
be cheap operators to do (in terms of what needs to be reevaluated)? No harm in
adding the full updown back in (it isn't clear how it got lost in the first
place).
Original comment by ramb...@gmail.com
on 18 Dec 2013 at 12:22
Increasing the weight of the "species-tree" operators may hurt analysis with a
smaller number of loci. Ideally the overall weights should be a some fixed
ratio (say 20%) of the total operators weight. We are trying to resolve this in
BEAST2 by introducing an "operators block" which can have a relative weight to
the other "blocks".
Original comment by jhe...@gmail.com
on 18 Dec 2013 at 12:45
Original comment by ramb...@gmail.com
on 18 Dec 2013 at 7:12
Original issue reported on code.google.com by
ramb...@gmail.com
on 17 Dec 2013 at 11:56