June 2009 Commit Log

Number of Commits:
57
Number of Active Developers:
6
dong.w.xie 2009-06-30 11:40 Rev.: 1816

BEAUTi: replace all dataType with getter.

97 lines of code changed in 11 files:

dong.w.xie 2009-06-29 17:19 Rev.: 1815

Renew Big Change of BEAUTi: update the structure containing multi-substitution models, multi-clock models, multi-tree models and priors.
The structure is PartitionData <=>
PartitionSubstitutionModel; PartitionData <=> PartitionClockModel; and PartitionData <=> PartitionTreeModel <=> PartitionTreePrior.
Given PD(i), there is PSM(0<j<=i), PCM(0<j<=i), PTM(0<k<=i), and PTP (l=1 or k). Also
PD~(PSM,PCM,PTM) and PTM~(PTP).

But updown operator does not init properly.

1489 lines of code changed in 13 files:

alexander.alekseyenko 2009-06-29 01:53 Rev.: 1814

adding the files missing from r1812

359 lines of code changed in 3 files:

msuchard 2009-06-29 00:51 Rev.: 1813

Typo (producing bug) fixed

1 lines of code changed in 1 file:

alexander.alekseyenko 2009-06-28 15:30 Rev.: 1812

Started a GUI for Bayes Factor Analysis of BEAST generated xml model.

744 lines of code changed in 8 files:

msuchard 2009-06-28 11:57 Rev.: 1811

Path sampling appears to be working for the testPathSampling.xml example! Yah! Harmonic mean estimators will soon be something of the past.

24 lines of code changed in 3 files:

msuchard 2009-06-28 06:22 Rev.: 1810

Add branch attribute providers that report direction of diffusion, distance and rate along each branch

1 lines of code changed in 1 file:

msuchard 2009-06-27 04:48 Rev.: 1809

A reversal of signs (of the time)

1 lines of code changed in 1 file:

msuchard 2009-06-27 01:30

Add branch attribute providers that report direction of diffusion, distance and rate along each branch

198 lines of code changed in 6 files:

dong.w.xie 2009-06-26 16:51 Rev.: 1806

Big Change of BEAUTi: finish the structure in GUI only, containing multi-substitution
models, multi-tree models and priors.
The structure is PartitionData <=>
PartitionSubstitutionModel; PartitionData <=> PartitionTreeModel <=>
PartitionTreePrior.
Given PD(i), there is PSM(0<j<=i), PTM(0<k<=i), and PTP (l=1 or k). Also
PD~(PSM,PTM) and PTM~(PTP).

Function and generator not completed.

307 lines of code changed in 8 files:

msuchard 2009-06-26 12:58 Rev.: 1805

Add a branch attribute provider that reports direction of diffusion along branch

102 lines of code changed in 2 files:

msuchard 2009-06-26 09:17 Rev.: 1804

Figured out how to integrate out internal and root node states quickly for continuous trait likelihood models

1491 lines of code changed in 13 files:

jheled 2009-06-25 12:04 Rev.: 1803

Add piecewise exponential to EBSP. add Brownian Motion prior to support it.

397 lines of code changed in 7 files:

jheled 2009-06-25 06:55 Rev.: 1802

more automatic intelliJ

180 lines of code changed in 17 files:

jheled 2009-06-25 06:54 Rev.: 1801

get rid of cyclic dependency. Add setting of population sizes to initial species tree.

396 lines of code changed in 8 files:

jheled 2009-06-25 06:14 Rev.: 1800

add missing module

2 lines of code changed in 1 file:

jheled 2009-06-25 05:38 Rev.: 1799

Fix string representation for cases without bounds or an id.

9 lines of code changed in 1 file:

dong.w.xie 2009-06-24 18:13 Rev.: 1798

Big Change of BEAUTi: to create a structure containing multi-substitution models, multi-tree models and priors.
The structure is PartitionData <=>
PartitionSubstitutionModel; PartitionData <=> PartitionTreeModel <=> PartitionTreePrior.
Given PD(i), there is PSM(0<j<=i), PTM(0<k<=i), and PTP (l=1 or k). Also PD~(PSM,PTM) and PTM~(PTP).

Not completed.

1122 lines of code changed in 15 files:

jheled 2009-06-23 09:12 Rev.: 1797

Darn typo (thanks Andrew)

348 lines of code changed in 3 files:

jheled 2009-06-23 08:10 Rev.: 1796

Change name. Was an acronym since it is experimental and may go away.

348 lines of code changed in 3 files:

jheled 2009-06-23 07:21 Rev.: 1795

move explicit strings to constants

31 lines of code changed in 1 file:

jheled 2009-06-23 07:20 Rev.: 1794

automatic idea changes, change type return type of getChild

215 lines of code changed in 36 files:

jheled 2009-06-23 07:15 Rev.: 1793

Add consistency check

15 lines of code changed in 1 file:

jheled 2009-06-23 06:59 Rev.: 1792

Correct return type of getChild(string)

13 lines of code changed in 1 file:

dong.w.xie 2009-06-19 17:20 Rev.: 1791

BEAUTi: separate init parameters and operators method according to partition series classes (PartitionData =>
PartitionSubstitutionModel => PartitionTreeModel => PartitionTreePrior)

221 lines of code changed in 4 files:

dong.w.xie 2009-06-19 14:35 Rev.: 1790

BEAUTi: rename partition series classes, and final relation is PartitionData => PartitionSubstitutionModel => PartitionTreeModel => PartitionTreePrior.

2864 lines of code changed in 28 files:

dong.w.xie 2009-06-19 10:36 Rev.: 1789

BEAUTi: Rename DataPartition into PartitionData, and add PartitionPopulation, to create the structure of PartitionData => PartitionModel => PartitionTree => PartitionPopulation.

1646 lines of code changed in 19 files:

dong.w.xie 2009-06-18 12:09 Rev.: 1787

BEAUTi: make Trait panel enable to change trait values, and trait table set focus on the selected trait during shifting between panels.

42 lines of code changed in 1 file:

dong.w.xie 2009-06-18 11:03 Rev.: 1786

BEAUti: make Log File and Tree Log File name updated together with File Stem Name.

15 lines of code changed in 1 file:

dong.w.xie 2009-06-18 10:18 Rev.: 1785

BEAUTi: before implement new model in BEAST, disable Yule and Birth Death for gene tree in Tree panel, when checked "use tip dates" in Tip Dates panel.

25 lines of code changed in 2 files:

dong.w.xie 2009-06-17 17:13 Rev.: 1784

Fix more BEAUTi bugs for *BEAST: the xml was incorrectly generated in Molecular Clock models (Autocorrelated Lognormal and Random Local Clock)

60 lines of code changed in 4 files:

dong.w.xie 2009-06-17 14:36 Rev.: 1783

Fix BEAUTi bugs for *BEAST:
1) attribute meanInRealSpace for <logNormalDistributionModel> contains prefix and make BEAST crash;
2) the calculation of branchRates.categories was incorrect for multi-partition with different taxa numbers;
3) the xml was incorrectly generated in Molecular Clock models, especially Relaxed Clock.

108 lines of code changed in 3 files:

dong.w.xie 2009-06-17 12:05 Rev.: 1782

Fix BEAUTi bugs:
1) add Number of Taxa column for each partition in Data Partition panel, in order to display taxa information for multi-partition models;
2) make Status Message update after remove species trait.

55 lines of code changed in 4 files:

dong.w.xie 2009-06-16 17:00 Rev.: 1781

More for GTR parameter test

61 lines of code changed in 1 file:

dong.w.xie 2009-06-16 16:57 Rev.: 1780

More work on GTR parameter estimation test.

86 lines of code changed in 1 file:

dong.w.xie 2009-06-15 15:46 Rev.: 1779

BEAUTi: change message Multispecies Coalescent analysis into *BEAST.

2 lines of code changed in 2 files:

dong.w.xie 2009-06-15 10:12 Rev.: 1778

Fix BEAUTi bug: The .frequencies parameters aren't being logged for the partition models, because BEAUTi isn't generating those lines.

11 lines of code changed in 1 file:

dong.w.xie 2009-06-15 09:58 Rev.: 1777

Rename Jeffreys prior to 1/x prior everywhere in Beauti, and leave it as option for people that know when its valid and want to use it.

2 lines of code changed in 1 file:

dong.w.xie 2009-06-12 16:34 Rev.: 1776

Correct BEAUti writeLogToFile where the line to generate GTR parameters log for Tracer had been accidently commented out.

1 lines of code changed in 1 file:

alexei.drummond 2009-06-12 16:21 Rev.: 1775

little things

416 lines of code changed in 4 files:

dong.w.xie 2009-06-12 15:20 Rev.: 1774

Fix BEAUTi bug: combo Number of Gamma Categories should be disable when the initial value of combo Site Heterogeneity is None.

9 lines of code changed in 1 file:

dong.w.xie 2009-06-12 10:38 Rev.: 1773

Finally fix the compile error r1770 this time

2 lines of code changed in 2 files:

dong.w.xie 2009-06-12 10:33 Rev.: 1772

To fix compile error

1 lines of code changed in 1 file:

dong.w.xie 2009-06-12 10:28 Rev.: 1771

To fix compile error r1770.

5 lines of code changed in 1 file:

dong.w.xie 2009-06-11 16:02 Rev.: 1770

Further work of GTR parameter estimation test

120 lines of code changed in 2 files:

dong.w.xie 2009-06-10 12:18 Rev.: 1769

Fix a BEAUti bug: species tree prior parameters updating incorrectly.

19 lines of code changed in 1 file:

dong.w.xie 2009-06-08 17:39 Rev.: 1768

Create GTR parameter estimation test

126 lines of code changed in 1 file:

dong.w.xie 2009-06-08 17:36

Refactory BeautiTester

553 lines of code changed in 3 files:

msuchard 2009-06-06 05:30 Rev.: 1765

Put back in conditioning check, as Philippe is still reporting some conditioning issues with the discrete-location-prior models.

16 lines of code changed in 1 file:

dong.w.xie 2009-06-05 09:48 Rev.: 1764

Fix the bug in r1763

2 lines of code changed in 1 file:

dong.w.xie 2009-06-05 09:43 Rev.: 1763

BEAUti species analysis: Yule model needs special treatment to generate N "1" and 2(N-1) "0", where N is the number of species.

14 lines of code changed in 1 file:

dong.w.xie 2009-06-04 16:51 Rev.: 1762

Fix BEAUti bug for Yule model in species tree.

109 lines of code changed in 3 files:

dong.w.xie 2009-06-04 09:40 Rev.: 1761

Fix bug in BEAUti and BEAST for Multispecies Coalescent analysis.

13 lines of code changed in 2 files:

dong.w.xie 2009-06-03 11:42 Rev.: 1760

BEAUTI species analysis work:
add Yule model for species tree prior.

70 lines of code changed in 6 files:

rambaut 2009-06-03 09:08 Rev.: 1759

Made some changes to the BEAGLE/BEAST interface to reflect the new BEAGLE API.

176 lines of code changed in 10 files:

rambaut 2009-06-03 09:07 Rev.: 1758

Fixed an issue in BEAUti not finding a PNG because a class had been moved. Also added an attempt to load the Quaqua look-and-feel which provides a nicer file dialog box on the Mac. This happens at runtime and shouldn't affect compilation or running if the library isn't available.

45 lines of code changed in 3 files:

dong.w.xie 2009-06-02 10:13 Rev.: 1757

Refactory BEAUTI package structure, add few panel packages and util package.

2780 lines of code changed in 44 files:

May 2009 »

Generated by StatSVN 0.7.0