April 2013 Commit Log

Number of Commits:
65
Number of Active Developers:
6
tbcbedford@gmail.com 2013-04-30 22:12 Rev.: 5621

Ignore this. Testing homebrew upgrade mechanisms.

1 lines of code changed in 2 files:

mdhall272@gmail.com 2013-04-30 03:37 Rev.: 5620

Added spatial kernel function; fixed bug.

107 lines of code changed in 2 files:

msuchard 2013-04-29 03:42 Rev.: 5619

Added missing CompoundParameter.fireParameterChangedEvent method, and demonstrating a nicer approach to multi-developer debugging.

33 lines of code changed in 4 files:

baele.guy@gmail.com 2013-04-28 23:45 Rev.: 5618

Reverted to how the parameters were set previously, the likelihoods were not being updated correctly.

26 lines of code changed in 1 file:

msuchard 2013-04-28 06:43 Rev.: 5617

Stream-lining serial operations during multi-parameter updates

49 lines of code changed in 3 files:

mdhall272@gmail.com 2013-04-27 00:31 Rev.: 5616

bug fixed

27 lines of code changed in 1 file:

mdhall272@gmail.com 2013-04-26 22:23 Rev.: 5615

bug fixed

31 lines of code changed in 1 file:

mdhall272@gmail.com 2013-04-26 20:36 Rev.: 5614

Done up to tracking down a few bugs

235 lines of code changed in 3 files:

fbielejec 2013-04-26 04:45 Rev.: 5613

static access to indices

14 lines of code changed in 9 files:

fbielejec 2013-04-26 04:42 Rev.: 5612

checks on values

81 lines of code changed in 11 files:

fbielejec 2013-04-25 22:57 Rev.: 5611

gamma + inv

21 lines of code changed in 4 files:

msuchard 2013-04-25 06:38 Rev.: 5610

Implemented a scaled mixture of Wishart distribution for precision matrix inference.

444 lines of code changed in 12 files:

fbielejec 2013-04-25 03:39 Rev.: 5609

new icon

13 lines of code changed in 5 files:

fbielejec 2013-04-25 03:33 Rev.: 5608

use those icons

56 lines of code changed in 13 files:

fbielejec 2013-04-25 02:59 Rev.: 5607

take max TO value as site count to avoid exceptions being thrown

53 lines of code changed in 8 files:

fbielejec 2013-04-24 21:29 Rev.: 5606

bug fixes in codon model XML generation

15 lines of code changed in 3 files:

mdhall272@gmail.com 2013-04-24 05:20 Rev.: 5605

Big and hopefully final rewrite

351 lines of code changed in 3 files:

rambaut 2013-04-24 00:23 Rev.: 5604

Finished tipdate precision for Pathogen. Now shows these as error bars (the points are given a date that is midpoint within the specified precision).

154 lines of code changed in 5 files:

rambaut 2013-04-23 21:44 Rev.: 5603

Adding date precision to the BEAUti/Pathogen date guessing panel

107 lines of code changed in 3 files:

msuchard 2013-04-23 14:39 Rev.: 5602

Added a half-T-distribution for more flexible specification of precision matrices in trait evolution.

189 lines of code changed in 3 files:

fbielejec 2013-04-20 02:21 Rev.: 5601

updated buildfile

12 lines of code changed in 4 files:

tbcbedford@gmail.com 2013-04-19 11:05 Rev.: 5600

Change "mergeColumns" to "mergeSerumIsolates" to agree with the rest of the spec.

6 lines of code changed in 2 files:

msuchard 2013-04-19 06:30 Rev.: 5599

Debugging flag to check for thread-level parallelization of likelihood evaluations

15 lines of code changed in 4 files:

rambaut 2013-04-18 23:15 Rev.: 5598

DiscreteTraitBranchRateModel parser tweaks.

62 lines of code changed in 3 files:

rambaut 2013-04-18 22:35 Rev.: 5597

DiscreteTraitBranchRateModel parser tweaks.

2 lines of code changed in 1 file:

fbielejec 2013-04-18 22:28 Rev.: 5596

added inverse gaussian clock and offset parameters to relaxed clocks. Still needs to be tested

92 lines of code changed in 3 files:

msuchard 2013-04-18 08:47 Rev.: 5594

Reimplemented lazy evaluation in Skygrid and cleaned up formatting.

497 lines of code changed in 4 files:

fbielejec 2013-04-17 02:41 Rev.: 5593

Inverse gaussian model in UI. Need to implement XML and command line options

28 lines of code changed in 2 files:

msuchard 2013-04-16 07:24 Rev.: 5592

Changing default behaviour to original.

3 lines of code changed in 2 files:

msuchard 2013-04-16 07:21 Rev.: 5591

Passing eigendecomposition condition number checking up to XML level.

25 lines of code changed in 1 file:

msuchard 2013-04-15 09:25 Rev.: 5590

Fixed Jacobian for log-transforms under new adaptive multivariate transition kernel for mixture models.

4 lines of code changed in 4 files:

mdhall272@gmail.com 2013-04-13 03:20 Rev.: 5589

C2CTL now implements treeTraitProvider and outputs painted trees

90 lines of code changed in 6 files:

fbielejec 2013-04-13 01:48 Rev.: 5588

help menu about dialog

42 lines of code changed in 4 files:

fbielejec 2013-04-13 01:37 Rev.: 5587

help menu

317 lines of code changed in 8 files:

tbcbedford@gmail.com 2013-04-12 22:16 Rev.: 5586

Fix bug in indexing. Proper number of columns now being recorded.

1 lines of code changed in 1 file:

fbielejec 2013-04-12 21:03 Rev.: 5585

custom edit menu

91 lines of code changed in 4 files:

fbielejec 2013-04-12 20:33 Rev.: 5584

custom edit menu

4 lines of code changed in 4 files:

fbielejec 2013-04-12 04:18 Rev.: 5583

fixed small bug in XML generator

13 lines of code changed in 2 files:

fbielejec 2013-04-12 03:18 Rev.: 5582

seed setting in CLI

21 lines of code changed in 1 file:

fbielejec 2013-04-11 22:59 Rev.: 5581

seed setting in UI

72 lines of code changed in 6 files:

fbielejec 2013-04-11 00:13 Rev.: 5580

working on multiple partitions in CLI.

14 lines of code changed in 1 file:

fbielejec 2013-04-11 00:02 Rev.: 5579

multiple partitions in CLI.

38 lines of code changed in 1 file:

mdhall272@gmail.com 2013-04-10 23:57 Rev.: 5578

Finished combining the classes.

23 lines of code changed in 3 files:

baele.guy@gmail.com 2013-04-10 23:45 Rev.: 5577

Fixed the MH ratio for the independent coalescent sampler.

16 lines of code changed in 2 files:

fbielejec 2013-04-10 23:39 Rev.: 5576

working on multiple partitions in CLI.

350 lines of code changed in 9 files:

mdhall272@gmail.com 2013-04-10 04:06 Rev.: 5575

continuing the clean-up

422 lines of code changed in 2 files:

baele.guy@gmail.com 2013-04-10 02:01 Rev.: 5574

Then LG model can also be used in the ancestral sequence annotator.

7 lines of code changed in 2 files:

baele.guy@gmail.com 2013-04-10 01:52 Rev.: 5573

Added LG model to the test package.

3 lines of code changed in 2 files:

baele.guy@gmail.com 2013-04-10 01:48 Rev.: 5572

Allow the BEAGLE parser to use the LG amino acid model.

2 lines of code changed in 2 files:

baele.guy@gmail.com 2013-04-10 01:46 Rev.: 5571

Allow the BEAST parser to use the LG amino acid model.

2 lines of code changed in 2 files:

baele.guy@gmail.com 2013-04-10 01:45 Rev.: 5570

Added LG model to the available types.

1 lines of code changed in 2 files:

baele.guy@gmail.com 2013-04-10 01:44 Rev.: 5569

Added the LG model of amino acid evolution (Le and Gascuel, 2008).

329 lines of code changed in 1 file:

mdhall272@gmail.com 2013-04-09 04:42 Rev.: 5568

FC2CTL reworked to calculate overall likelihoods and randomly pick a transmission tree when MCMC samples are taken, similarly to discrete traits. Still probably too slow unless the likelihood function can be solved analytically. Will probably fold that class into the main C2CTL as a variant.

90 lines of code changed in 3 files:

fbielejec 2013-04-09 00:37 Rev.: 5567

Parameter values in CLI.

185 lines of code changed in 2 files:

baele.guy@gmail.com 2013-04-09 00:30 Rev.: 5566

Allows for an independent coalescent to be drawn given a list of taxa and a demographic model. The generated tree is then copied into the existing treeModel.

171 lines of code changed in 1 file:

baele.guy@gmail.com 2013-04-09 00:25 Rev.: 5565

New version of an additional method to copy a proposed tree into the current treeModel.

19 lines of code changed in 1 file:

baele.guy@gmail.com 2013-04-08 23:54 Rev.: 5564

Bug fix when using prior sampling to estimate (log) marginal likelihoods.

3 lines of code changed in 2 files:

mdhall272@gmail.com 2013-04-08 21:15 Rev.: 5563

Nomenclature change, continued

4 lines of code changed in 2 files:

mdhall272@gmail.com 2013-04-08 20:41 Rev.: 5562

Nomenclature change

508 lines of code changed in 7 files:

msuchard 2013-04-06 05:50 Rev.: 5561

Example of logging

41 lines of code changed in 1 file:

msuchard 2013-04-06 05:29 Rev.: 5560

Example of lazy evaluation after tree change events.

27 lines of code changed in 1 file:

msuchard 2013-04-06 05:11 Rev.: 5559

Reconstructions from AncestralStateBeagleTreeLikelihood now follow useAmbiguities=true/false setting.

26 lines of code changed in 6 files:

mdhall272@gmail.com 2013-04-06 03:57 Rev.: 5558

Tidying up

23 lines of code changed in 1 file:

mdhall272@gmail.com 2013-04-06 03:48 Rev.: 5557

Made the case class an inner class of the case set class, which is much neater.

294 lines of code changed in 5 files:

tbcbedford@gmail.com 2013-04-02 05:05 Rev.: 5556

Finalizing schema to agree with paper. Row effects -> Virus effects. Column effects -> Serum effects. Also, reordering input file to be: virus isolate, virus strain, virus year, serum isolate, serum strain, serum year, titre.

23 lines of code changed in 1 file:

March 2013 »

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