trunk: solve Issue 523: BEAUti Traits panel buttons enable/disable should adapt to data and traits
20 lines of code changed in 1 file:
trunk: correct *BEAST calibration and solve Issue 520: BEAUti tmrca parameter not sync with prior panel.
1 lines of code changed in 1 file:
update testSRD06 xml
289 lines of code changed in 2 files:
Skeleton for Gaussian Process coalescent model
300 lines of code changed in 5 files:
Start towards implementing Volz et al (2009) Genetics
246 lines of code changed in 4 files:
Latest version of GMRFMultilocusSkyrideLikelihood. Needs to be cleaned up.
17 lines of code changed in 1 file:
trunk: correct *BEAST calibration and solve Issue 520: BEAUti tmrca parameter not sync with prior panel.
25 lines of code changed in 8 files:
trunk: correct *BEAST calibration on species tree XML generator in BEAUti.
109 lines of code changed in 4 files:
Fixed optional parameter settings in GMRFSkyrideLikelihoodParser
1 lines of code changed in 2 files:
trunk: implement *BEAST calibration on species tree XML generator in BEAUti.
187 lines of code changed in 5 files:
Better way to handle star trees via a derived TreeModel
661 lines of code changed in 4 files:
Update to allow multiple input files with marginal likelihood samples to be processed.
67 lines of code changed in 1 file:
Removed some unnecessary comments.
0 lines of code changed in 1 file:
Update to allow multiple input files with marginal likelihood samples to be processed.
57 lines of code changed in 1 file:
trunk: update Species Set panel GUI part to take Taxa object instead, and ready to implement XML generator next time.
315 lines of code changed in 5 files:
Preliminary star tree implementation as an alternative to the correlated trait models; would function better as a subclass of TreeModel than TreeLikelihood.
553 lines of code changed in 6 files:
Can still edit a trait called 'species' if it is not currently being used for *BEAST
1 lines of code changed in 2 files:
trunk: Issue 514: NullPointerException when setting prior to tree model in BEAUti Prior panel
1 lines of code changed in 1 file:
Updated the multilocus gmrf model so that we have a proper prior. Still needs to be cleaned up a little bit.
265 lines of code changed in 2 files:
trunk: Issue 513: *BEAST constraint of the 'species' trait
2 lines of code changed in 1 file:
trunk: finish Species Set panel GUI part, and wait for XML example to implement XML generator.
65 lines of code changed in 1 file:
Fixed an issue with repeatedly added listeners for Prior Dialog components.
7 lines of code changed in 2 files:
Added drag and drop of XML file to input file text of main beast dialog boxl.
12 lines of code changed in 1 file:
Fixed an issue with creating a 'species' trait when *BEAST was already on. Now checks that the user actually loads a species trait when asked to when switching on *BEAST.
Also, reinstated UCLN and UCED as clock options. UCGD and UCCD (Chauchy) are not currently implemented but could be. Also autocorrelated?
132 lines of code changed in 4 files:
Fixed warning messages
2 lines of code changed in 1 file:
Removed certain special cases that weren't necessary
2 lines of code changed in 1 file:
trunk: initial dev for Species Set panel when *BEAST calibration that is only allowed on species tree
839 lines of code changed in 4 files:
A slight modification to the thread pooling. Rather than just threading the 'likelihood' compoundLikelihood, it now threads the 'posterior'. To do this it flattens out all the compoundLikelihoods (i.e., 'likelihood' and 'prior'). Should allow the prior calculations to help pad some of the unused thread and load balance a bit better. Tested and works but would like to do some benchmarking.
38 lines of code changed in 4 files:
Refined the interface for turning on and off *BEAST. 'species' is not a special trait until *BEAST is turned on.
61 lines of code changed in 16 files:
trunk: solve Issue 510: BEAUti uncheck *BEAST but cannot reverse to normal BEAST properly
30 lines of code changed in 6 files:
trunk: solve Issue 506: The gamma prior is not reverted to what it was previously if *BEAST in unselected.
0 lines of code changed in 2 files:
trunk: solve Issue 503: BEAUti operator analysis should be chosen as default
1 lines of code changed in 1 file:
BEAUti generates discrete trait XMLs that run.
137 lines of code changed in 4 files:
Adding binary stochastic Dollo to BEAUti. Now can read Ringe dataset and generate an XML that runs.
499 lines of code changed in 11 files:
added parser for IntermediateExchange.
64 lines of code changed in 1 file:
trunk: update xml to compare BEAST 2.
318 lines of code changed in 3 files: