March 2013 Commit Log

Number of Commits:
93
Number of Active Developers:
9
rambaut 2013-03-30 10:00 Rev.: 5555

Caching of rates doesn't seem to work with multiple partitions so turning it off now. The lazy computation of these (which does work) should prevent large overheads of computing these repeatedly at operator time (which was considerable when using gamma distributions due to the numerical quantile finding).

32 lines of code changed in 2 files:

julia.pal.r@gmail.com 2013-03-29 13:12 Rev.: 5554

update ready for Marc to show me

90 lines of code changed in 1 file:

julia.pal.r@gmail.com 2013-03-29 05:26 Rev.: 5553

adding elements to store-restore

44 lines of code changed in 3 files:

fbielejec 2013-03-28 23:48 Rev.: 5552

basic CLI options with some exception handling. Moving to parameter values.

208 lines of code changed in 5 files:

dong.w.xie@gmail.com 2013-03-28 11:48 Rev.: 5551

more improvement of SeqGen

26 lines of code changed in 2 files:

alexei.drummond 2013-03-28 11:02 Rev.: 5550

Rearranging code in SeqGen to speed it up a bit for very large trees (100,000 tips)

5 lines of code changed in 1 file:

fbielejec 2013-03-28 02:55

starting to implement CLI

203 lines of code changed in 7 files:

philippe.lemey@gmail.com 2013-03-28 01:22 Rev.: 5547

Transmission statistic now updates the transmission history and accomodates estimated transmission times

1 lines of code changed in 2 files:

philippe.lemey@gmail.com 2013-03-28 00:56 Rev.: 5546

text message changes for the renaissance counting method in AncestralStatesOptionsPanel

1 lines of code changed in 1 file:

msuchard 2013-03-27 06:44 Rev.: 5545

Fixed memory allocation bug introduced in previous commit.

1 lines of code changed in 2 files:

msuchard 2013-03-27 03:48 Rev.: 5544

Implemented a log-determinant routine for numerical stability and fixed getParameterValue in DiagonalMatrix

857 lines of code changed in 5 files:

msuchard 2013-03-27 03:29 Rev.: 5543

Fix to issue 687; may need to port to 1.7 branch. RandomWalkOperator no longer reflects negative values when using default bounds.

15 lines of code changed in 4 files:

julia.pal.r@gmail.com 2013-03-26 06:36 Rev.: 5542

small change

23 lines of code changed in 2 files:

rambaut 2013-03-26 05:04 Rev.: 5541

<trait> element in Tree Logger can now take a filter="XXX" attribute instead of specifying a particular name to log all traits that starts with a particular string. Also if the <trait> element has neither a name or a filter attribute then all traits are logged.

67 lines of code changed in 1 file:

fbielejec 2013-03-26 03:34 Rev.: 5540

new icon

0 lines of code changed in 1 file:

fbielejec 2013-03-26 02:24 Rev.: 5539

fixed small bug

24 lines of code changed in 7 files:

fbielejec 2013-03-26 01:43 Rev.: 5538

loading saved data with new trees panel

135 lines of code changed in 17 files:

fbielejec 2013-03-25 22:44 Rev.: 5537

update taxa column when data changes

51 lines of code changed in 4 files:

fbielejec 2013-03-25 11:37 Rev.: 5536

remove unwanted taxa when tree table changes

48 lines of code changed in 7 files:

fbielejec 2013-03-25 09:14 Rev.: 5535

some updates to UI

33 lines of code changed in 5 files:

fbielejec 2013-03-25 08:43 Rev.: 5534

new tree table

225 lines of code changed in 8 files:

fbielejec 2013-03-25 04:18 Rev.: 5533

labels on buttons

174 lines of code changed in 7 files:

baele.guy@gmail.com 2013-03-24 01:04 Rev.: 5532

First version of an additional method to copy a proposed tree (for example, from the coalescentSimulator) into the current treeModel. At the moment, copying rates and traits is not yet implemented. These may need to be copied during a separate tree traversal, if the direct access to leftChild and rightChild cannot be circumvented ...

63 lines of code changed in 1 file:

julia.pal.r@gmail.com 2013-03-23 09:39 Rev.: 5531

Complete phase1

24 lines of code changed in 1 file:

julia.pal.r@gmail.com 2013-03-23 07:40 Rev.: 5530

working on summary - need to calculate "sigmoidal" medians, etc

148 lines of code changed in 6 files:

julia.pal.r@gmail.com 2013-03-23 04:33 Rev.: 5529

added the "tracer" analysis similar to EBSP

495 lines of code changed in 7 files:

fbielejec 2013-03-23 04:03 Rev.: 5528

working on new trees panel

97 lines of code changed in 7 files:

fbielejec 2013-03-23 03:20 Rev.: 5527

improved rendering of tables

111 lines of code changed in 7 files:

fbielejec 2013-03-23 02:24

working on new trees panel

498 lines of code changed in 12 files:

fbielejec 2013-03-23 00:04 Rev.: 5524

reset idrefs after writing to XML

91 lines of code changed in 6 files:

fbielejec 2013-03-22 20:36 Rev.: 5523

missing hashCode method

5 lines of code changed in 2 files:

fbielejec 2013-03-22 09:07 Rev.: 5522

removing siteCount from UI

189 lines of code changed in 7 files:

fbielejec 2013-03-22 00:33 Rev.: 5521

removing siteCount from UI

148 lines of code changed in 9 files:

fbielejec 2013-03-22 00:10

no need for site count, this information can be parsed from partitions

50 lines of code changed in 7 files:

fbielejec 2013-03-21 23:45 Rev.: 5518

fixed some XML issues

150 lines of code changed in 3 files:

julia.pal.r@gmail.com 2013-03-21 05:55 Rev.: 5517

Special logger

49 lines of code changed in 3 files:

fbielejec 2013-03-21 03:46 Rev.: 5516

compare newick strings to see if models are equal

16 lines of code changed in 3 files:

fbielejec 2013-03-21 03:25 Rev.: 5515

no need for lower and upper bounds

106 lines of code changed in 2 files:

fbielejec 2013-03-21 02:50 Rev.: 5514

adding relaxed clock models to XML generator

81 lines of code changed in 3 files:

fbielejec 2013-03-21 01:25 Rev.: 5513

adding relaxed clock models

50 lines of code changed in 2 files:

msuchard 2013-03-20 12:29 Rev.: 5512

Fixed transform; they were missing Jacobians in computing densities.

154 lines of code changed in 9 files:

fbielejec 2013-03-20 10:28 Rev.: 5511

changed nucleotide freq model param names

74 lines of code changed in 2 files:

baele.guy@gmail.com 2013-03-19 21:31 Rev.: 5510

Added transformations to the syntax rules of the adaptable variance MVN operator.

5 lines of code changed in 1 file:

msuchard 2013-03-19 18:02 Rev.: 5509

Fixed log determinate for large diagonal matrices; refactored transforms.

363 lines of code changed in 9 files:

fbielejec 2013-03-19 11:29 Rev.: 5508

disable taxa panel when second analysis selected

87 lines of code changed in 6 files:

fbielejec 2013-03-19 09:56 Rev.: 5507

cleaning up and simplifying the code

309 lines of code changed in 6 files:

fbielejec 2013-03-19 09:04 Rev.: 5506

cleaning up and simplifying the code

169 lines of code changed in 9 files:

julia.pal.r@gmail.com 2013-03-19 05:49 Rev.: 5505

works -fixed Slice sampling detail

126 lines of code changed in 1 file:

julia.pal.r@gmail.com 2013-03-19 03:57 Rev.: 5504

a working version for fixed genealogy

19 lines of code changed in 1 file:

fbielejec 2013-03-19 03:34 Rev.: 5503

update taxa panel upon loading

28 lines of code changed in 4 files:

fbielejec 2013-03-19 03:07 Rev.: 5502

fixed a small bug

17 lines of code changed in 2 files:

fbielejec 2013-03-19 02:35 Rev.: 5501

still not ideal but better

7 lines of code changed in 1 file:

fbielejec 2013-03-19 02:19 Rev.: 5500

this works but sets the columns again which is not ideal

49 lines of code changed in 1 file:

fbielejec 2013-03-19 01:48 Rev.: 5499

working on loading serialized data

157 lines of code changed in 2 files:

fbielejec 2013-03-19 01:22 Rev.: 5498

move code initialising Editors to listeners

62 lines of code changed in 4 files:

fbielejec 2013-03-19 00:41 Rev.: 5497

allow for one instance of Editors at once

24 lines of code changed in 7 files:

fbielejec 2013-03-18 22:56 Rev.: 5496

working on loading serialized data

44 lines of code changed in 7 files:

fbielejec 2013-03-18 21:11 Rev.: 5495

keep choices set in Editors

147 lines of code changed in 10 files:

julia.pal.r@gmail.com 2013-03-17 23:27 Rev.: 5494

like GibbsOperator --not the right thing to do but temporal solution

74 lines of code changed in 2 files:

julia.pal.r@gmail.com 2013-03-16 06:09 Rev.: 5493

updating

13 lines of code changed in 1 file:

julia.pal.r@gmail.com 2013-03-16 04:37 Rev.: 5492

just updating - need to see why infty in SliceSampler. It fails in Oldscore vs currentScore

49 lines of code changed in 2 files:

baele.guy@gmail.com 2013-03-16 04:10 Rev.: 5491

More flexible version of the adaptable variance MVN operator with respect to the transformations, which can now be provided using XML specification.

160 lines of code changed in 1 file:

julia.pal.r@gmail.com 2013-03-15 15:48 Rev.: 5490

Parameterizing a lot and changes in number of latents, location of latents..need to fix GP sampling of one point, problem with "last" neighbor

376 lines of code changed in 3 files:

fbielejec 2013-03-14 23:50 Rev.: 5489

working on updating GUI to reflect loaded inputs

34 lines of code changed in 4 files:

rambaut 2013-03-14 08:34 Rev.: 5488

Some serious effort to build a post-analysis tool for antigenic mapping.

1367 lines of code changed in 17 files:

fbielejec 2013-03-14 03:21 Rev.: 5487

working on loading serialized inputs to bss

104 lines of code changed in 4 files:

fbielejec 2013-03-14 02:57 Rev.: 5486

working on serializing inputs to bss

6 lines of code changed in 1 file:

fbielejec 2013-03-14 02:46 Rev.: 5485

simplifying implementation

76 lines of code changed in 8 files:

fbielejec 2013-03-14 01:52 Rev.: 5484

looking for source of serialization exception

20 lines of code changed in 4 files:

fbielejec 2013-03-14 00:46 Rev.: 5483

working on serialization

89 lines of code changed in 2 files:

rambaut 2013-03-14 00:00 Rev.: 5482

Created an 'AttributeBranchRateModel' which exposes an attribute embedded in a tree as a branch rate model.

158 lines of code changed in 7 files:

fbielejec 2013-03-13 22:49 Rev.: 5481

working on serialization

154 lines of code changed in 5 files:

rambaut 2013-03-13 08:37 Rev.: 5480

Added caching of quantiles of rate categories and lazy computation (to avoid repeated computation of these).

22 lines of code changed in 1 file:

julia.pal.r@gmail.com 2013-03-13 05:50 Rev.: 5479

fixed coalescent interval in Likelihood suff. stat and small testing to Block Update

33 lines of code changed in 2 files:

tbcbedford@gmail.com 2013-03-13 03:49 Rev.: 5478

This is a refactor of AntigenicLikelihood. It's been slimmed down substantially. I've tried to cut down on the all the redirection involved in setting up parameters. There is now just equal-sized vectors of names, locations, offsets and effects for both viruses and sera. "Column effects" and locations now have to refer to the same set of entities, unlike previously where locations could refer to strains and effects could refer to isolates.

This is currently broken in some way and giving "SEVERE: State was not correctly calculated after an operator move." errors.

781 lines of code changed in 1 file:

rambaut 2013-03-13 00:12 Rev.: 5477

Temporarily removed EmpricialTrees implementation of BranchRateModel as it was confusing the TreeLikelihood parser (which picked it up as the first BranchRateModel even when it is not being used as such).

3 lines of code changed in 1 file:

msuchard 2013-03-12 08:53 Rev.: 5476

Improved error checking for binomial likelihood parser.

6 lines of code changed in 2 files:

julia.pal.r@gmail.com 2013-03-12 06:39 Rev.: 5475

Fixed updating the likelihood

9 lines of code changed in 1 file:

rambaut 2013-03-11 01:12 Rev.: 5474

Some serious effort to build a post-analysis tool for antigenic mapping.

2064 lines of code changed in 18 files:

rambaut 2013-03-07 21:58 Rev.: 5473

Undepricating this class for simple BMDS.

1 lines of code changed in 2 files:

rambaut 2013-03-07 21:56 Rev.: 5472

EmpiricalTreeDistributionModel can now read a rate attribute and expose it as a branchRateModel (it now implements that interface).

74 lines of code changed in 3 files:

julia.pal.r@gmail.com 2013-03-06 06:39 Rev.: 5471

added prior of hyperparameters to "likelihood" wrong but functional, don't want to add a Parser for a mixture prior

17 lines of code changed in 1 file:

fbielejec 2013-03-05 02:57 Rev.: 5470

save/load settings menu items

72 lines of code changed in 5 files:

fbielejec 2013-03-05 02:05 Rev.: 5469

file filter for imports

48 lines of code changed in 1 file:

fbielejec 2013-03-05 02:04 Rev.: 5468

working on XML import

162 lines of code changed in 8 files:

baele.guy@gmail.com 2013-03-04 21:47 Rev.: 5467

New version of the adaptable variance MVN operator. Transformation to the log scale is currently always performed, the Jacobian has been taken into account for the MH-ratio.

59 lines of code changed in 1 file:

msuchard 2013-03-04 16:17 Rev.: 5466

Fixed bounds that individual parameters induce when constrained equal.

36 lines of code changed in 2 files:

msuchard 2013-03-03 15:46 Rev.: 5465

Prototype Parameter.class to constraint equality among parameters; seems more consistent with usage than a Model.class

293 lines of code changed in 4 files:

julia.pal.r@gmail.com 2013-03-03 11:11 Rev.: 5464

testing GPBlockUpdate -trying to understand Prior value

349 lines of code changed in 3 files:

julia.pal.r@gmail.com 2013-03-02 12:56 Rev.: 5463

small changes

5 lines of code changed in 1 file:

julia.pal.r@gmail.com 2013-03-02 08:02 Rev.: 5462

small changes

48 lines of code changed in 1 file:

msuchard 2013-03-01 16:40 Rev.: 5461

Prototype Model.class to constraint equality among parameters.

146 lines of code changed in 2 files:

dong.w.xie@gmail.com 2013-03-01 15:19 Rev.: 5460

tracer: big correction of tracer code for my previous development on "Conditional Posterior Distributions", which fixed bugs in GUI especially in Filter, and use EDT thread.

260 lines of code changed in 22 files:

February 2013 »

Generated by StatSVN 0.7.0