Directory src/dr/app/beauti/types/

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rambaut 2013-05-10 03:29 Rev.: 5642

Added parsing and setting of date precisions in BEAUti plus generation of uniform sampling within these bounds. Also fixed the date calculations so Jan 1st (say 2013) is 2013.0.

2 lines of code changed in 2 files:

• src/dr/app/beauti/types: TipDateSamplingType.java (+2 -1)

msuchard 2012-04-20 09:52 Rev.: 4926

Fixed issue 621: BEAUti now provides unbounded logPopSizes and an initial value on the correct scale.

28 lines of code changed in 2 files:

• src/dr/app/beauti/types: PriorScaleType.java (new)

dong.w.xie 2011-11-25 13:46 Rev.: 4491

trunk:solve Issue 549: BeautiOptions.updateAll() stop user to customize clock rates

2 lines of code changed in 2 files:

• src/dr/app/beauti/types: FixRateType.java (new)

rambaut 2011-11-20 07:28 Rev.: 4456

Refactoring of the robust counting and sequence error model into a new tab ('States') which allows these options to be specified on a per partition basis. These options are still not finished yet but the panel can be hidden using the constant at the top of BeautiFrame.

2 lines of code changed in 2 files:

• src/dr/app/beauti/types: BinaryModelType.java (new)

dong.w.xie 2011-11-14 16:34 Rev.: 4416

trunk: solve Issue 538: move tree prior panel to the left of table, and Issue 539: use the same background in citation text area in Tree panel, and some more code for calibrated Yule

48 lines of code changed in 2 files:

• src/dr/app/beauti/types: PriorType.java (new)

dong.w.xie 2011-11-08 16:55 Rev.: 4398

trunk: start BEAUti dev Calibrated Yule

2 lines of code changed in 2 files:

• src/dr/app/beauti/types: TreePriorType.java (new)

rambaut 2011-11-05 02:53 Rev.: 4390

More cleaning up and adjusting of uniform priors.

8 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+8 -1)

rambaut 2011-11-03 21:34 Rev.: 4386

Fixed issue 530: http://code.google.com/p/beast-mcmc/issues/detail?id=530. Now allows marginal prior on root height to be switched off.

42 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+42 -36)

rambaut 2011-11-01 21:59 Rev.: 4384

Trying to fix up the confusion with uniform bounds. The parameter object in beauti now has 'uniformUpper' and 'uniformLower' rather than using the truncationUpper/Lower (uniform prior cannot be truncated now). Changed the logPDF function of UniformDistribution to take the log before the reciprocal to reduce chance of underflow (note however that taking the log of Double.MAX_VALUE (or twice that if the lower bound is -MAX_VALUE) may still fail). Testing now being undertaken...

1 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+1 -1)

rambaut 2011-10-12 03:12 Rev.: 4352

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?

90 lines of code changed in 1 file:

• src/dr/app/beauti/types: OldClockType.java (new 90)

msuchard 2011-10-08 19:39 Rev.: 4342

Adding binary stochastic Dollo to BEAUti. Now can read Ringe dataset and generate an XML that runs.

9 lines of code changed in 1 file:

• src/dr/app/beauti/types: BinaryModelType.java (+9 -6)

rambaut 2011-09-16 04:23 Rev.: 4317

Fixing up discrete/continuous trait generation..

0 lines of code changed in 1 file:

• src/dr/app/beauti/types: DiscreteSubstModelType.java (del)

rambaut 2011-09-16 03:04 Rev.: 4316

Continuous traits nearly working. Separated discrete traits out into a 'component' but will have broken things probably. Fixing up now.

1 lines of code changed in 3 files:

• src/dr/app/beauti/types: ContinuousSubstModelType.java (del), OperatorType.java (new)

msuchard 2011-09-12 21:57 Rev.: 4305

Fixes to HPM specification in BEAUti

1 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+1 -1)

rambaut 2011-09-09 22:55 Rev.: 4301

Adding continuous traits in BEAUti

20 lines of code changed in 1 file:

• src/dr/app/beauti/types: ContinuousSubstModelType.java (new 20)

msuchard 2011-09-09 06:05 Rev.: 4299

Fixed prior graphs in BEAUti, inverse gamma cdf and started stochastic Dollo

1 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+1 -1)

rambaut 2011-08-19 00:53 Rev.: 4201

Work on discrete Antigenic MDS

2 lines of code changed in 2 files:

• src/dr/app/beauti/types: SequenceErrorType.java (new)

rambaut 2011-07-29 05:20 Rev.: 4133

Cleaned up selection of tree priors available for different situations.

3 lines of code changed in 1 file:

• src/dr/app/beauti/types: TreePriorType.java (+3 -3)

rambaut 2011-07-28 11:42 Rev.: 4130

Removed CTMC reference prior checkbox from clock model table (you select this in the improved prior dialog). Also moved note about this in tooltip for this checkbox to a text area that appears in the PriorDialog when this prior is selected.

1 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+1 -1)

rambaut 2011-06-25 04:09 Rev.: 4068

Some major refactoring of PriorDialog. Probably horribly broken but at least it compiles.

66 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+66 -66)

rambaut 2011-06-24 20:49 Rev.: 4062

Some serious cleaning up of how priors are specified. This allows appropriate prior choices for different 'flavours' of parameters (non-negative, zero-one interval, discrete, HPM, CMTC rates). Truncation of the the prior is now a switch and bounds so can be applied to any prior (although the UI is not in place for this yet).

125 lines of code changed in 3 files:

• src/dr/app/beauti/types: ParameterFlavour.java (new 16), PriorScaleType.java (-1), PriorType.java (+109 -78)

msuchard 2011-06-22 17:04 Rev.: 4059

Mostly working hierarchical phylogenetic models

32 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+32 -20)

rambaut 2011-06-22 01:40 Rev.: 4057

Cleaned up PriorDialog to better render distributions if possible.

69 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+69 -61)

msuchard 2011-06-19 15:55 Rev.: 4044

Added (approx.) conditional reference prior for overall substitution rate scalar into BEAUti

7 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+7)

msuchard 2011-06-04 04:19 Rev.: 4003

Initial work on implementing hierarchical priors into BEAUti

37 lines of code changed in 2 files:

• src/dr/app/beauti/types: HierarchicalModelType.java (new 22), PriorType.java (+15 -1)

dong.w.xie 2011-03-31 13:07 Rev.: 3908

Trunk: more big update on BEAUti microsat.

1 lines of code changed in 1 file:

• src/dr/app/beauti/types: OperatorType.java (+1)

dong.w.xie 2011-03-30 16:45 Rev.: 3907

Trunk: continue to work on BEAUti microsat, but writing different taxa function still has a bug.

4 lines of code changed in 2 files:

• src/dr/app/beauti/types: MicroSatModelType.java (+4 -3)

dong.w.xie 2011-03-28 17:06 Rev.: 3905

Trunk: big update in BEAUti micro-sat.

44 lines of code changed in 2 files:

• src/dr/app/beauti/types: MicroSatModelType.java (+43 -8), OperatorType.java (+1)

dong.w.xie 2011-03-25 16:23 Rev.: 3902

Trunk: finish Brith Death Serial Sampling in BEAUti, but some of xmls are not running.

16 lines of code changed in 2 files:

• src/dr/app/beauti/types: PriorScaleType.java (+1), PriorType.java (+15 -1)

dong.w.xie 2011-03-25 12:10 Rev.: 3900

Trunk: continue to implement Brith Death Serial Sampling in BEAUti.

1 lines of code changed in 1 file:

• src/dr/app/beauti/types: TreePriorType.java (+1 -1)

dong.w.xie 2011-03-24 15:55 Rev.: 3899

Trunk: start to implement Brith Death Serial Sampling in BEAUti.

3 lines of code changed in 1 file:

• src/dr/app/beauti/types: TreePriorType.java (+3)

dong.w.xie 2011-03-21 10:46 Rev.: 3886

Trunk: recover uniformLower and uniformUpper, and lower upper will be used as hard bound only. It solves Issue 409: BEAUti should explicitly generate uniform priors.

6 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+6 -6)

dong.w.xie 2011-03-14 16:27 Rev.: 3872

Trunk: more work on micro-sat data in BEAUti.

2 lines of code changed in 1 file:

• src/dr/app/beauti/types: MicroSatModelType.java (+2 -1)

dong.w.xie 2011-03-10 16:30 Rev.: 3864

Trunk: start to make micro-satellite available in BEAUti panels.

20 lines of code changed in 1 file:

• src/dr/app/beauti/types: MicroSatModelType.java (+20)

dong.w.xie 2010-12-13 16:49 Rev.: 3748

Trunk: more for Issue 434

2 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+2 -2)

dong.w.xie 2010-12-13 16:38 Rev.: 3747

Trunk: solve Issue 434: BEAUti: Initial value missing from prior dialog

4 lines of code changed in 1 file:

• src/dr/app/beauti/types: PriorType.java (+4 -4)

rambaut 2010-10-28 22:44 Rev.: 3686

Cleaning up BEAUti a bit.

4 lines of code changed in 2 files:

• src/dr/app/beauti/types: ClockType.java (+4 -4)

dong.w.xie 2010-10-26 11:45 Rev.: 3677

Trunk: correct spelling.

1 lines of code changed in 2 files:

• src/dr/app/beauti/types: ClockDistributionType.java (new)

rambaut 2010-10-26 04:14 Rev.: 3676

Only write one general substitution data type per discrete substitution model.

20 lines of code changed in 2 files:

• src/dr/app/beauti/types: DiscreteSubstModelType.java (new 20), LocationSubstModelType.java (del)

rambaut 2010-10-23 03:56 Rev.: 3664

This is a very large commit. It addresses some architectural issues in BEAUti that were going to hinder implementation of continuous traits.

The main thing it does is to isolate creating and importing traits from creating partitions on those traits. A button on the data panel explicitly specifies that a trait should be used as a data partition (i.e., have a TreeLikelihood). This allows traits to be used for other purposes (such as defining Species in *BEAST). This has also allowed considerable simplification of code and tidying up.

There are a number of bug fixes as well over v1.6.0 that I will add to the issue list to keep track of them. Given the complex nature of these changes, I do not think these should be ported to the 1.6.0 branch but perhaps the bugs can be fixed.

These changes will have introduced bugs and possibly cause issues with XML generation that now need to be fixed (I will attempt to catch as many as possible).

888 lines of code changed in 21 files:

• src/dr/app/beauti/types: BinaryModelType.java (+43), ClockDistributionType.java (+45), ClockType.java (+55), FixRateType.java (+46), FrequencyPolicyType.java (+44), LocationSubstModelType.java (new 20), OperatorType.java (+73), PopulationSizeModelType.java (new), PriorScaleType.java (+34), PriorType.java (+244), RelativeRatesType.java (new), SequenceErrorType.java (+28), StartingTreeType.java (new), TipDateSamplingType.java (+21), TreePriorParameterizationType.java (new), TreePriorType.java (+52)