December 2011 Commit Log

Number of Commits:
63
Number of Active Developers:
7
dong.w.xie 2011-12-22 10:19 Rev.: 4564

trunk: update README

4 lines of code changed in 1 file:

rambaut 2011-12-22 03:17 Rev.: 4563

Fixed the HTML in the about box.

3 lines of code changed in 1 file:

rambaut 2011-12-22 02:32 Rev.: 4562

Updated native libraries for Mac release.

0 lines of code changed in 11 files:

rambaut 2011-12-21 22:43 Rev.: 4561

Minor text edit.

2 lines of code changed in 2 files:

rambaut 2011-12-21 22:42 Rev.: 4560

Updated the developers list.

9 lines of code changed in 1 file:

rambaut 2011-12-21 22:10 Rev.: 4559

Updated MacOSX make file. Notionally makes a fat library containing 32bit, 64bit and PPC code.

16 lines of code changed in 2 files:

rambaut 2011-12-21 22:00 Rev.: 4558

Updated MacOSX make file. Notionally makes a fat library containing 32bit, 64bit and PPC code. Have commented out the PPC version as I can't compile it (on Lion). Will try to make it conditional on PPC compiler being available. Probably a good idea to distribute a full fat version as binary.

41 lines of code changed in 2 files:

rambaut 2011-12-21 19:33 Rev.: 4557

Fix for Issue 88: a check that the resampling frequency is a multiple of the original sampling frequency.

11 lines of code changed in 1 file:

dong.w.xie 2011-12-21 15:04 Rev.: 4556

trunk: update version history

40 lines of code changed in 1 file:

dong.w.xie 2011-12-20 12:43 Rev.: 4555

trunk: add microsatellite data and xml example

1035 lines of code changed in 2 files:

dong.w.xie 2011-12-20 12:25 Rev.: 4554

trunk:solve Issue 548: Beauti does not generate functional xml for msat data analysis

53 lines of code changed in 6 files:

graham853@gmail.com 2011-12-20 04:19 Rev.: 4553

Randomized initialisation of sequence assignments in AlloppSpeciesBindings. Less strict numerical test in AlloppNetworkPrior.

10 lines of code changed in 2 files:

tbcbedford@gmail.com 2011-12-19 01:01 Rev.: 4552

Fixed typo.

2 lines of code changed in 2 files:

tbcbedford@gmail.com 2011-12-19 00:57 Rev.: 4551

Updated the text describing AICM and Bayes factor model comparison. Always doing comparisons on ln scale. Also, in keeping with previous behavior, simple harmonic mean estimator is never used. Options are: "aicm" and "harmonic mean". Harmonic mean gives smoothed estimator.

28 lines of code changed in 4 files:

tbcbedford@gmail.com 2011-12-16 23:28 Rev.: 4550

Model comparison now defaults to comparing all open trace files, rather than all selected trace files. To me this seems like a more expected behavior. I tried to implement a checkbox in the dialog box for "Use selected trace files only". However, this was difficult because the List<TraceList> that's passed in from TracerFrame doesn't have information about what is currently selected.

10 lines of code changed in 2 files:

rambaut 2011-12-16 23:19 Rev.: 4549

Ratios of AICMs are not Bayes factors.

3 lines of code changed in 1 file:

msuchard 2011-12-16 05:37 Rev.: 4548

Bayes factors are not odds.

3 lines of code changed in 1 file:

tbcbedford@gmail.com 2011-12-16 02:54 Rev.: 4547

Moving naming from "Bayes Factors" to "Model Comparison"

8 lines of code changed in 4 files:

dong.w.xie 2011-12-15 15:13 Rev.: 4546

trunk:solve Issue 565: hasIdenticalTaxa(List<AbstractPartitionData> partitionDataList) gives wrong boolean

6 lines of code changed in 2 files:

dong.w.xie 2011-12-15 13:38 Rev.: 4545

trunk:solve Issue 446: no indication that Checkboxes and rate text boxes are not editable in Clock Group table

18 lines of code changed in 1 file:

tbcbedford@gmail.com 2011-12-15 06:06 Rev.: 4544

Tweaking colors to make Tracer plots less garish. Feel free to roll this back if you're unhappy.

Before: http://imgur.com/1BpFx,UQkAl#0
After: http://imgur.com/1BpFx,UQkAl#1

4 lines of code changed in 3 files:

tbcbedford@gmail.com 2011-12-15 04:17 Rev.: 4543

Full width table by default.

0 lines of code changed in 1 file:

tbcbedford@gmail.com 2011-12-15 04:05 Rev.: 4542

Implementing AICM in Tracer. The Bayes factor dialog now has a drop-down menu with AICM as the default option.

109 lines of code changed in 6 files:

msuchard 2011-12-13 16:26 Rev.: 4541

Force all sequences into upper-case.

6 lines of code changed in 2 files:

dong.w.xie 2011-12-13 11:07 Rev.: 4540

trunk:solve Issue 541: BEAUti generates wrong xml when enforcing a uniform prior on node ages, and add a nexus example with user specified starting tree

78 lines of code changed in 5 files:

dong.w.xie 2011-12-12 12:10 Rev.: 4539

trunk: tidy up native/ folder but it needs Andrew to update all Makefiles before deleting compile scripts

1305 lines of code changed in 14 files:

fbielejec 2011-12-12 11:21 Rev.: 4538

reverting r4531

0 lines of code changed in 1 file:

rambaut 2011-12-12 10:56

Restored (but renamed to improve clarity) the UI to enable state counting other than the dNdS Robust Counting.

56 lines of code changed in 7 files:

dong.w.xie 2011-12-12 10:30 Rev.: 4535

trunk: revert r4509 but keep the changes in r4529

8 lines of code changed in 1 file:

fbielejec 2011-12-12 09:59 Rev.: 4534

this import breaks my build and is apparently not neccessary

1 lines of code changed in 1 file:

fbielejec 2011-12-12 09:52 Rev.: 4533

use dndsRobustCounting for consistency

3 lines of code changed in 1 file:

fbielejec 2011-12-12 09:52 Rev.: 4532

added merge patterns tag

1 lines of code changed in 1 file:

fbielejec 2011-12-12 09:52 Rev.: 4531

should we add mergePatterns for dnds robust counting here?

3 lines of code changed in 1 file:

fbielejec 2011-12-12 09:51

fixing dnds robust counting

55 lines of code changed in 4 files:

dong.w.xie 2011-12-09 10:03 Rev.: 4526

trunk:solve Issue 562: BEAUTi : Birth Death Epidemiology Model update

130 lines of code changed in 3 files:

sibon.li 2011-12-08 11:39 Rev.: 4525

Improved presentation for AncestralSequenceAnnotator and GetAncestralSequenceFromSplitTrait

14 lines of code changed in 3 files:

msuchard 2011-12-08 04:58 Rev.: 4524

Integrated mixture models

214 lines of code changed in 2 files:

dong.w.xie 2011-12-07 15:37 Rev.: 4523

trunk: remove wrong dependency to dr.evomodel.newtreelikelihood.TreeLikelihood which is not used by main BEAST

4 lines of code changed in 2 files:

rambaut 2011-12-07 11:27 Rev.: 4522

New parameterization of Tanja's BDSSM for epidemiology

17 lines of code changed in 1 file:

dong.w.xie 2011-12-07 11:13 Rev.: 4521

trunk: move the remaining native folder under the root of project for easy finding.

13601 lines of code changed in 46 files:

dong.w.xie 2011-12-07 11:07 Rev.: 4520

trunk: delete duplicate native folder

0 lines of code changed in 24 files:

dong.w.xie 2011-12-07 10:58 Rev.: 4519

trunk:solve Issue 559: BEAUti throws exception if adding any additional partition with different taxa when already having data partitions

1 lines of code changed in 1 file:

rambaut 2011-12-07 10:49 Rev.: 4518

New parameterization of Tanja's BDSSM for epidemiology

172 lines of code changed in 3 files:

dong.w.xie 2011-12-07 10:45 Rev.: 4517

trunk:solve Issue 558: duplicate method to check different taxa in BEAUti and Issue 557: Removing a partition doesn't remove its unique taxa

75 lines of code changed in 10 files:

tbcbedford@gmail.com 2011-12-07 05:20 Rev.: 4516

Small cleanup and starting to store trajectory with HybridTauleapSEIR class.

80 lines of code changed in 1 file:

tbcbedford@gmail.com 2011-12-07 04:53 Rev.: 4515

Integreting Denise's code for forward simulation of SIR trajectories.

507 lines of code changed in 3 files:

rambaut 2011-12-06 17:08 Rev.: 4514

Commented out the printing of the entire HI table to screen

9 lines of code changed in 1 file:

rambaut 2011-12-06 16:50 Rev.: 4513

Bug in updating locations for tips.

1 lines of code changed in 1 file:

rambaut 2011-12-06 16:41 Rev.: 4512

DATL wasn't initializing the locations of the tree tips.

11 lines of code changed in 1 file:

dong.w.xie 2011-12-06 16:09 Rev.: 4511

more

3 lines of code changed in 1 file:

dong.w.xie 2011-12-06 16:01 Rev.: 4510

trunk: make consistent between 2 native folder, we need to delete one

5 lines of code changed in 4 files:

dong.w.xie 2011-12-06 15:04 Rev.: 4509

trunk: correct getPrefix in AncestralStatesComponentGenerator

10 lines of code changed in 1 file:

dong.w.xie 2011-12-06 12:09 Rev.: 4508

trunk: solve Issue 555: Does sequence error model have to apply to every sequence data partition?

30 lines of code changed in 3 files:

dong.w.xie 2011-12-06 10:35 Rev.: 4507

trunk: solve Issue 466: Cannot run beauti / beast from git-svn clone

5 lines of code changed in 1 file:

dong.w.xie 2011-12-05 16:19 Rev.: 4506

trunk: more fixes of Issue 556: BEAUti "birth-death serially sampled model" correction required

20 lines of code changed in 1 file:

dong.w.xie 2011-12-05 14:21 Rev.: 4505

trunk: some fixes of Issue 556: BEAUti "birth-death serially sampled model" correction required

3 lines of code changed in 1 file:

dong.w.xie 2011-12-05 13:52 Rev.: 4504

trunk:solve Issue 475: BEAUti hypervariable models do not fill in all necessary model attributes to run, and Issue 554: SequenceErrorModelComponentOptions did not create parameters properly

30 lines of code changed in 6 files:

dong.w.xie 2011-12-05 11:43 Rev.: 4503

trunk:solve Issue 451: BEAST suggests using a non-integer for randomWalkIntegerOperator

2 lines of code changed in 2 files:

rambaut 2011-12-04 10:45 Rev.: 4502

Fixed Issue 519, http://code.google.com/p/beast-mcmc/issues/detail?id=519 where changing values in for uniform in prior dialog would cause a hang. The issue was that the dialog was wrapping the uniformDistribution in a TruncatedDistribution which then cause terrible problems with the numerical inverse PDF estimator. Now obeys the isTruncatable flag.

1 lines of code changed in 1 file:

rambaut 2011-12-04 10:43 Rev.: 4501

Added a dialog box to rename a partition if it has the same name as an existing partition.

144 lines of code changed in 5 files:

rambaut 2011-12-04 10:41 Rev.: 4500

Fixed an issue where once a 'substitutions' TreeLogger was created all subsequent TreeLoggers were also using the same BranchRates model to do substitution trees. This was an issue in the parser. The issue would not manifest itself if the substitutions tree log was the last in the XML (as generated by BEAUti).

4 lines of code changed in 1 file:

dong.w.xie 2011-12-01 11:08 Rev.: 4499

trunk:solve Issue 502: BEAUti prior panel: the lognormal prior chart cannot accept negative numbers for M=log(mean), but it should

4 lines of code changed in 1 file:

dong.w.xie 2011-12-01 09:16 Rev.: 4498

trunk:solve Issue 553: BEAUti sampling on all individual tips should use randomWalkOperator

1 lines of code changed in 1 file:

November 2011 »

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