March 2011 Commit Log

Number of Commits:
74
Number of Active Developers:
8
dong.w.xie 2011-03-31 17:52 Rev.: 3910

Trunk: update doc.

65 lines of code changed in 3 files:

dong.w.xie 2011-03-31 16:53 Rev.: 3909

Trunk: BEAUti microsat works, but XML is not working in BEAST because of transition probability entry out of bound.

37 lines of code changed in 8 files:

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

Trunk: more big update on BEAUti microsat.

171 lines of code changed in 23 files:

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.

240 lines of code changed in 15 files:

dong.w.xie 2011-03-29 15:53 Rev.: 3906

Trunk: finally make Birth Death Serially Sampling model working in BEAUti, by adding some function to calculate initial values for model parameters.

35 lines of code changed in 4 files:

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

Trunk: big update in BEAUti micro-sat.

368 lines of code changed in 15 files:

akaruiws 2011-03-28 10:28 Rev.: 3904

Create set methods for max and min.

8 lines of code changed in 1 file:

denise.kuehnert@gmail.com 2011-03-25 17:45 Rev.: 3903

some testing / debugging (unfinished)

60 lines of code changed in 1 file:

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.

152 lines of code changed in 10 files:

denise.kuehnert@gmail.com 2011-03-25 14:31 Rev.: 3901

231 lines of code changed in 1 file:

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

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

482 lines of code changed in 5 files:

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

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

159 lines of code changed in 8 files:

jheled 2011-03-24 13:20 Rev.: 3898

validation for RPN expressions

57 lines of code changed in 6 files:

dong.w.xie 2011-03-24 09:41 Rev.: 3897

Trunk: fix a pattern generator bug.

3 lines of code changed in 1 file:

dong.w.xie 2011-03-23 17:16 Rev.: 3896

Trunk: make auto scale function to fix BEAUti partition framework, which moves it from priorOptions into partitionOptions.getParameter(), and discard priorOptions.

223 lines of code changed in 17 files:

dong.w.xie 2011-03-23 12:16 Rev.: 3895

Trunk: fix more bugs.

25 lines of code changed in 5 files:

dong.w.xie 2011-03-23 11:24 Rev.: 3894

Trunk: solve Issue 445: BEAUti: clock rate configuration is not consistent between clock model panel and prior panel

107 lines of code changed in 7 files:

dong.w.xie 2011-03-22 16:15 Rev.: 3893

Trunk: solve Issue 427: BEAUti generates a mergePatterns even when it is enclosing a single patterns element

126 lines of code changed in 4 files:

dong.w.xie 2011-03-22 12:52 Rev.: 3892

Trunk: solve Issue 426: BEAUti does not preserve settings when re-linking, and Issue 444: BEAUti: model table select row not update.

154 lines of code changed in 11 files:

dong.w.xie 2011-03-22 10:11 Rev.: 3891

Trunk: solve Issue 443: BEAUti: change alpha default prior into Exponential mean=0.5 offset=0.0.

10 lines of code changed in 1 file:

dong.w.xie 2011-03-22 09:38 Rev.: 3890

Trunk: uniform bounds validation and some comments.

13 lines of code changed in 1 file:

dong.w.xie 2011-03-22 09:25 Rev.: 3889

Trunk: fix many small bugs, e.g. alignment generator generate null, prior dialog did not read default vaule, clock uniform needs default uniform bounds.

15 lines of code changed in 5 files:

dong.w.xie 2011-03-21 17:18 Rev.: 3888

Trunk: keep working on clock model group.

66 lines of code changed in 3 files:

dong.w.xie 2011-03-21 11:23 Rev.: 3887

Trunk: more for Issue 409: BEAUti should explicitly generate uniform priors.

50 lines of code changed in 8 files:

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.

56 lines of code changed in 8 files:

msuchard 2011-03-21 07:57 Rev.: 3885

Tracking down numerical instability for very long and very short simulation times under Hobolth's algorithm

11 lines of code changed in 1 file:

msuchard 2011-03-21 07:36 Rev.: 3884

Parameter dimension check for arbitrary branch rates

7 lines of code changed in 1 file:

philippe.lemey@gmail.com 2011-03-19 07:51 Rev.: 3883

reverting ContourMaker in TimeSlicer back to no bandwidth limit

4 lines of code changed in 2 files:

philippe.lemey@gmail.com 2011-03-18 22:34 Rev.: 3882

adding ContourMaker with bandwidth limit to TimeSlicer

34 lines of code changed in 1 file:

dong.w.xie 2011-03-18 17:53 Rev.: 3881

Trunk: working on operators and generator.

209 lines of code changed in 13 files:

dong.w.xie 2011-03-17 16:03 Rev.: 3880

Trunk: make clock model group working in GUI, but operators and generator not working yet.

147 lines of code changed in 6 files:

msuchard 2011-03-17 11:27 Rev.: 3879

Higher precision needed to check for CTMC connectedness with large state spaces.

3 lines of code changed in 1 file:

msuchard 2011-03-17 10:51 Rev.: 3878

Tweaks to 2D KDEs.

27 lines of code changed in 5 files:

dong.w.xie 2011-03-16 16:48 Rev.: 3877

Trunk: big change of implementing clock model group, including to correct some auto GUI event regarding "fix mean" and calibration. Not finished yet.

397 lines of code changed in 11 files:

dong.w.xie 2011-03-16 09:53 Rev.: 3876

Trunk: solve Issue 442: BEAUti: taxon set table does not refresh after changing tree model.

915 lines of code changed in 5 files:

dong.w.xie 2011-03-15 17:14 Rev.: 3875

Trunk: implement clock model group table in BEAUti, to solve the problem that "fix mean rate" function cannot be applied to the different types of clock models, for example, molecular clock ~ trait clock ~ microsatellite clock model.

202 lines of code changed in 3 files:

alexei.drummond 2011-03-15 09:15 Rev.: 3874

20 taxa, 7 constraints, 0.1seconds

16 lines of code changed in 2 files:

alexei.drummond 2011-03-14 22:08 Rev.: 3873

yes

228 lines of code changed in 3 files:

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

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

431 lines of code changed in 18 files:

alexei.drummond 2011-03-14 15:32 Rev.: 3871

count constrained ranked trees

231 lines of code changed in 1 file:

alexei.drummond 2011-03-12 17:59 Rev.: 3870

ranked forest

48 lines of code changed in 3 files:

alexei.drummond 2011-03-12 15:39 Rev.: 3869

ranked forest

361 lines of code changed in 2 files:

alexei.drummond 2011-03-11 15:39 Rev.: 3868

325 lines of code changed in 2 files:

dong.w.xie 2011-03-11 14:03 Rev.: 3867

Trunk: correct a bug in BeautiImpoter that stops BEAUti framework to load micro-sat data, and make framework to recognize data type by searching partitions.

57 lines of code changed in 4 files:

dong.w.xie 2011-03-11 12:03 Rev.: 3866

Trunk: refactory BEAUti framework.

64 lines of code changed in 9 files:

dong.w.xie 2011-03-11 11:09 Rev.: 3865

Trunk: fix a bug in MicroSatImporter when loading diploid locus data.

74 lines of code changed in 4 files:

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

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

72 lines of code changed in 5 files:

dong.w.xie 2011-03-10 12:11 Rev.: 3863

Trunk: make micro-satellite file successfully loaded in BEAUti data panel.
Start to use jdk1.6 code.

259 lines of code changed in 9 files:

dong.w.xie 2011-03-09 17:32 Rev.: 3862

Trunk: micro-satellite importer for BEAUti.

142 lines of code changed in 3 files:

alexei.drummond 2011-03-09 10:25 Rev.: 3861

seqgen generalization prep

55 lines of code changed in 4 files:

dong.w.xie 2011-03-08 15:15 Rev.: 3860

Trunk: big check-in to add micro-satellite in BEAUti.
1) Because it uses patterns not alignment, PartitionPattern is added, and PartitionData is still used for all previous data type.
2) getDataType is corrected to get actual data type, where traits are generalDataType, and trait name is getting from getDataDescription.
3) add MICRO_SAT data type.

456 lines of code changed in 29 files:

philippe.lemey@gmail.com 2011-03-05 01:16 Rev.: 3859

more DnDsPerSiteAnalysis tweaking

4 lines of code changed in 1 file:

dong.w.xie 2011-03-04 15:40 Rev.: 3858

Trunk: final version of TestCalibratedYuleModel.

21 lines of code changed in 1 file:

dong.w.xie 2011-03-04 09:33 Rev.: 3857

Trunk: add target to create beastTest.jar and change build into jdk 1.6 for BEAST 1.7.

11 lines of code changed in 1 file:

dong.w.xie 2011-03-04 09:31 Rev.: 3856

Trunk: make better file printer for plotting in test calibration yule model.

10 lines of code changed in 1 file:

alexei.drummond 2011-03-03 21:13 Rev.: 3855

59 lines of code changed in 1 file:

dong.w.xie 2011-03-03 17:13 Rev.: 3854

Trunk: test calibration yule model more with non disjoint trees error

268 lines of code changed in 3 files:

rambaut 2011-03-03 13:01 Rev.: 3853

Improved reporting

8 lines of code changed in 2 files:

alexei.drummond 2011-03-03 12:51 Rev.: 3852

changes

24 lines of code changed in 1 file:

rambaut 2011-03-03 12:35 Rev.: 3851

Hadn't fixed the problem with tip association to antigenic data. Now I have.

25 lines of code changed in 2 files:

dong.w.xie 2011-03-03 12:24 Rev.: 3850

Trunk: test calibration yule model

181 lines of code changed in 1 file:

rambaut 2011-03-03 10:26 Rev.: 3849

Realized that I was randomizing the association between antigenic data and tips of the tree. Fixed

24 lines of code changed in 2 files:

rambaut 2011-03-03 07:56 Rev.: 3848

More MDS work

100 lines of code changed in 4 files:

msuchard 2011-03-03 05:44 Rev.: 3847

Add functionality to read plink SNP frequencies and run continuous diffusion models

306 lines of code changed in 6 files:

philippe.lemey@gmail.com 2011-03-02 22:53 Rev.: 3846

mor DnDsPerSiteAnalysis tweaking

55 lines of code changed in 1 file:

msuchard 2011-03-02 14:27 Rev.: 3845

ID assigned in ReciprocalStatisticParser necessary to test normal-gamma model Gibbs samplers

1 lines of code changed in 2 files:

msuchard 2011-03-02 12:15 Rev.: 3844

Amino acid substitution model for influenza.

166 lines of code changed in 1 file:

dong.w.xie 2011-03-02 09:56 Rev.: 3843

Trunk: solve Issue 438: BEAST should tell you what frequencies belong to which partition

2 lines of code changed in 3 files:

philippe.lemey@gmail.com 2011-03-02 01:16 Rev.: 3842

DnDsPerSiteAnalysis tweaking

110 lines of code changed in 1 file:

dong.w.xie 2011-03-01 15:35 Rev.: 3841

Trunk: correct an error from previous check-in

2 lines of code changed in 2 files:

dong.w.xie 2011-03-01 15:17 Rev.: 3840

Trunk: solve Issue 420: Add error message : Partitions cannot have the same name

51 lines of code changed in 4 files:

dong.w.xie 2011-03-01 14:21 Rev.: 3839

Trunk: solve Issue 425: BEAUti can't re-link subst models anymore

14 lines of code changed in 2 files:

dong.w.xie 2011-03-01 10:49 Rev.: 3838

Trunk: solve Issue 433: Typo in BEAUTi and example files

2 lines of code changed in 2 files:

dong.w.xie 2011-03-01 09:43 Rev.: 3837

Trunk: solve Issue 432: More detail for error message: *BEAST special part generation has failed.

60 lines of code changed in 4 files:

February 2011 »

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