Andrew Rambaut

Results 62 comments of Andrew Rambaut

BEAUti weight for AVMVN transition kernel

I think probably the weight should simply be the number of parameters the AVMVN is controlling. Before, we down-weighted some parameters (i.e., kappa) because they mixed well and were expensive...

BEAUti weight for AVMVN transition kernel

Will push this for the next minor update...

BEAUti issues with very high resolution screen on Windows 10.

I think this is generally an issue with Oracle Java on Windows. Not sure there is much we can do here.

Explicitly allow setting of reconstructing states at tips

Should add an additional option to AncestralTraitParser - with a list of tip taxa to reconstruct on.

Explicitly allow setting of reconstructing states at tips

Combine the UI with that for #859 - add taxon sets for either TMRCA reconstructions or tip reconstructions.

Add half a year to sampling date when performing tip date sampling

I think this will need to just be a cosmetic thing in the tipdate table. Perhaps it would be better to show the range (i.e., "2004 - 2005")

Dollo model does not appear to parse under BEAGLE

Automatically turn off scaling with this model?

Remove all rate node parameters from tree model

I agree this should be done (also the node traits in TreeModel). Models wanting to store traits on trees should use a TreeParameterModel. However there are two areas that would...

Pick better starting values in BEAUti where scaled by tree size (i.e. pop-size)

Why is this an issue for this YFV - it uses constant population size, no? Can see this being an issue with more complex models. The issue: BEAUti can no...

Pick better starting values in BEAUti where scaled by tree size (i.e. pop-size)

I have generalized this issue. There are a number of parameters that could be given better starting values if the total tree height was known (to an order of magnitude)....