Andrew Rambaut

Migrate Ancestral States and Markov Jumps to TreeDataLikelihood

1

Currently AncestralStateBeagleTreeLikelihood and MarkovJumpsBeagleTreeLikelihood are in dr.evomodel.treelikelihood. We should think about how to migrate these abilities to treedatalikelihood (as plugins of some sort to extract realisations at logging).

Error creating 'nu' parameter with Amino Acid model?

4

I'm using BEAST v1.10.1, and have received the following error: Creating site rate model. Creating site rate model. Creating site rate model. Creating site rate model. Creating site rate model....

An option to give a rolling average over some number of steps for the time/step reporting.

As the title says.

Operator for uniform on pInv not created (and thus error thrown about not finding it).

BEAUti doesn't add 'nu' relative rates into amino acid siteModel elements

Make thread control behaviour more intuitive

1

BEAGLE 3's CPU kernel is multithreaded. The number of threads produced can be controlled on the command line using the `-beagle_thread_count` option. The previous `-threads` controls the number of BEAST...

Some antivirus software flags BEAST exes as possible trojans because they are wrapped using launch4j. The solution would be to code sign these executables. This may need to be done...

Implemented covariate loading for GLM-diffusion models, the machinery is there to do the same for fixed effects on rates (or any other parameter that is grouped/linked hierarchically).