Comments (6)
After pondering this issue for quite some time, the following requirements appear irreconcilable:
- hide any complexity from BEAUti users
- low impact on the core, preferably not adding classes or special constructs for connecting operators to subsets
- flexible specification of XML
The best thing I can think of is having BEAUti update operator weights on Species-related operators (easily identifiable by their associated partition being "Species") so that the sum of weights is approximately say about 20% of the total of operator weights. This update is required every time a new alignment is added or deleted, and would only affect the weights of the Species related operators. It would fit requirements 1 & 2, but fails 3.
from beast2.
Preferring to not add classes seems like a very un-object-oriented approach to adding functionality...
Sent from my iPhone
On 24/03/2014, at 10:02 AM, rbouckaert [email protected] wrote:
After pondering this issue for quite some time, the following requirements appear irreconcilable:
- hide any complexity from BEAUti users
- low impact on the core, preferably not adding classes or special constructs for connecting operators to subsets
- flexible specification of XML
The best thing I can think of is having BEAUti update operator weights on Species-related operators (easily identifiable by their associated partition being "Species") so that the sum of weights is approximately say about 20% of the total of operator weights. This update is required every time a new alignment is added or deleted, and would only affect the weights of the Species related operators. It would fit requirements 1 & 2, but fails 3.
—
Reply to this email directly or view it on GitHub.
from beast2.
I think relative weights will be a boon to BEAUti users, and should not be
hidden. So the only question is (2), i.e. low impact.
I am not sure why this is a high impact, but willing to take Remco word on
the matter.
Personally, I would prefer a "true" solution instead of another BEAST
hack, *even if BEAUti2 can't handle it at the moment. That is, a solution
along the lines I outlined for the XML, which would require manual editing
now, and perhaps later supported by BEAUti.
-Joseph
On 24 March 2014 10:02, rbouckaert [email protected] wrote:
After pondering this issue for quite some time, the following requirements
appear irreconcilable:
- hide any complexity from BEAUti users
- low impact on the core, preferably not adding classes or special
constructs for connecting operators to subsets- flexible specification of XML
The best thing I can think of is having BEAUti update operator weights on
Species-related operators (easily identifiable by their associated
partition being "Species") so that the sum of weights is approximately say
about 20% of the total of operator weights. This update is required every
time a new alignment is added or deleted, and would only affect the weights
of the Species related operators. It would fit requirements 1 & 2, but
fails 3.Reply to this email directly or view it on GitHubhttps://github.com//issues/17#issuecomment-38397180
.
from beast2.
It is easy enough to set up a CompoundParameter that has its own weight and takes a set of operators that it selects from using its own OperatorSchedule. That will result in XML close to the originally proposed -- but in the BEAST 2 dialect of course. The storeToFile and restoreFromFile methods need a bit of attention in order to assure parameter tuning is maintained after resuming an MCMC run.
from beast2.
--delete--
from beast2.
duplicate #633
from beast2.
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from beast2.