June 2010 Commit Log

Number of Commits:
89
Number of Active Developers:
6
msuchard 2010-06-30 10:13 Rev.: 3297

Tracer now uses a Gaussian KDE that performs very nicely

48 lines of code changed in 5 files:

msuchard 2010-06-30 00:27 Rev.: 3296

Tool for performing KDE using a Gaussian kernel (most standard approach)

418 lines of code changed in 4 files:

philippe.lemey@gmail.com 2010-06-29 11:28 Rev.: 3295

deleting MultiSpatial stuff

136 lines of code changed in 5 files:

philippe.lemey@gmail.com 2010-06-29 10:31 Rev.: 3294

extending GeoMultiSpatialDistribution to accomodate arrays of polygons defining a region

0 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-06-29 10:29 Rev.: 3293

extending GeoSpatialCollectionModel to accomodate arrays of polygons in a GeoMultiSpatialDistribution defining a region

0 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-06-28 17:01 Rev.: 3292

modifications to accomodate unconditional N and S counts per site

321 lines of code changed in 1 file:

msuchard 2010-06-26 08:11 Rev.: 3291

Changed default prior for clock.rate when data are sparse (1 site)

76 lines of code changed in 3 files:

msuchard 2010-06-26 05:42 Rev.: 3290

Bug fixed

42 lines of code changed in 1 file:

msuchard 2010-06-25 15:58 Rev.: 3289

Philippe, Vladimir and Marc are still trying to make robust counts nice

102 lines of code changed in 4 files:

akaruiws 2010-06-25 15:04 Rev.: 3288

Delete mountainLion directory.

0 lines of code changed in 1 file:

dong.w.xie 2010-06-25 12:28 Rev.: 3287

TRUNK: update XML examples for Issue 324: "rates" in "svsGeneralSubstitutionModel" should not have relativeTo

2 lines of code changed in 3 files:

dong.w.xie 2010-06-25 12:04 Rev.: 3286

TRUNK: update BEAUti for Issue 324: "rates" in "svsGeneralSubstitutionModel" should not have relativeTo

2 lines of code changed in 1 file:

dong.w.xie 2010-06-25 10:23 Rev.: 3285

TRUNK: solve Issue 324: "rates" in "svsGeneralSubstitutionModel" should not have relativeTo

5 lines of code changed in 1 file:

rambaut 2010-06-25 03:24 Rev.: 3284

Starting to integrate Marc's KDE additions into Tracer. To do this I have allowed DensityPanel to only display statistics of the same type (double, int or String) rather than just not display some statistics. KDE button only appears if continuous densities are being viewed. Next step I think is to cache KDE's to avoid recomputing.

870 lines of code changed in 7 files:

dong.w.xie 2010-06-24 11:51 Rev.: 3283

TRUNK: merge Issue 323: BEAUti: reload xml having alignments with different taxa

6 lines of code changed in 1 file:

msuchard 2010-06-24 03:52 Rev.: 3281

Modifying CodonPartitionedRobustCounting to differentiate between internal and external branches; minor optimization of uniformized state history simulation

110 lines of code changed in 5 files:

msuchard 2010-06-23 15:55 Rev.: 3280

Working on CodonPartitionedRobustCounting; a possible need for Uniformization

41 lines of code changed in 4 files:

msuchard 2010-06-23 02:16 Rev.: 3279

Forgot to wrapper one use of the KDE inside a compile-time remove flag.

3 lines of code changed in 1 file:

msuchard 2010-06-22 16:09 Rev.: 3278

Started work on KDEs in Tracer

500 lines of code changed in 7 files:

msuchard 2010-06-22 05:50 Rev.: 3277

Refactoring attribute to trait (for likelihood) parsing for use in other models

360 lines of code changed in 3 files:

dong.w.xie 2010-06-21 18:03 Rev.: 3276

TRUNK: BEAUti: fix a bug of tree log for discrete traits

3 lines of code changed in 2 files:

akaruiws 2010-06-18 18:45 Rev.: 3275

Importance sampling for the msat ancestral states.

1311 lines of code changed in 14 files:

dong.w.xie 2010-06-17 12:39 Rev.: 3274

TRUNK: BEAUti: more on log for discrete traits

45 lines of code changed in 2 files:

msuchard 2010-06-17 10:45 Rev.: 3273

Critical fix: branch rates now print out in tree log under new TreeTrait framework. Also starting to remove duplicated code from classes needing to output different combinations of TreeTrait summaries

408 lines of code changed in 16 files:

msuchard 2010-06-17 03:21 Rev.: 3272

Implemeneted amino acid models for BEAGLE

113 lines of code changed in 3 files:

msuchard 2010-06-16 13:54 Rev.: 3271

Add several wrappers to convert automatically between different reductions of TreeTraits (sum over tree, sum across sites, etc.). One can even double-wrap to get sum over tree + sum across sites. This should reduce substantial code-duplication and earn me a gold star.

172 lines of code changed in 1 file:

dong.w.xie 2010-06-15 11:59 Rev.: 3270

TRUNK: BEAUti: fix trait bug with integer type

6 lines of code changed in 1 file:

msuchard 2010-06-15 09:39 Rev.: 3269

Fixed bug in rewards; JUnitTests are awesome

6 lines of code changed in 3 files:

msuchard 2010-06-15 08:26 Rev.: 3268

Fixed store/restore of subordinated process for Uniformization; also fixed reward process for Uniformization

50 lines of code changed in 6 files:

msuchard 2010-06-15 06:49 Rev.: 3267

Tweaks for checking store/restore with ancestral states and Markov processes; I still do not understand why saving the ancestral states is unnecessary.

23 lines of code changed in 4 files:

msuchard 2010-06-14 15:14 Rev.: 3266

DiscreteTraitBranchRateModel now works with AncestralStateBeagleTreeLikelihood as well

21 lines of code changed in 2 files:

msuchard 2010-06-14 14:48 Rev.: 3265

DiscreteTraitBranchRateModel now works again for ancestral state reconstructions. Something is still wrong with AncestralStateBeagleTreeLikelihood however.

1 lines of code changed in 1 file:

msuchard 2010-06-14 14:20 Rev.: 3264

DiscreteTraitBranchRateModel now works again for ancestral state reconstructions. Something is still wrong with AncestralStateBeagleTreeLikelihood however.

85 lines of code changed in 7 files:

dong.w.xie 2010-06-14 12:47 Rev.: 3263

TRUNK: solve Issue 315: make alias "svsGeneralSubstitutionModel" of "generalSubstitutionModel", Issue 316: previous XML with "generalSubstitutionModel" is not working, and Issue 317: BEAUti: geo-phylogenetic symmetric + no BSSVS xml not working.

16 lines of code changed in 2 files:

rambaut 2010-06-13 23:31 Rev.: 3262

Added a 'backbone' local clock to LocalClockModel (sorry it took so long Philippe).

79 lines of code changed in 3 files:

akaruiws 2010-06-13 21:50 Rev.: 3261

Weighted random walk integer operators.

309 lines of code changed in 6 files:

dong.w.xie 2010-06-13 20:06 Rev.: 3260

TRUNK: new tracer: fixing changing trace type bug.

26 lines of code changed in 3 files:

msuchard 2010-06-13 05:51 Rev.: 3259

Better caching in subordinated process for Uniformization

8 lines of code changed in 1 file:

msuchard 2010-06-13 04:48 Rev.: 3258

Better immediate calculation caching for MarkovJumps

80 lines of code changed in 3 files:

rambaut 2010-06-13 03:10 Rev.: 3257

Trying a reparameterization of DTBRM

1 lines of code changed in 1 file:

rambaut 2010-06-13 03:05 Rev.: 3256

Additional work on DiscreteTraitBranchRateModel - adding an indicator parameter to provide link between state and rate.

12 lines of code changed in 2 files:

rambaut 2010-06-12 22:52 Rev.: 3255

Trying a reparameterization of DTBRM

54 lines of code changed in 2 files:

rambaut 2010-06-12 22:09 Rev.: 3254

Additional work on DiscreteTraitBranchRateModel - adding an indicator parameter to provide link between state and rate.

43 lines of code changed in 4 files:

rambaut 2010-06-12 03:59 Rev.: 3253

Prettied-up the printing of diagnostic message for a zero initial likelihood (actually this is a port of a improvement from the BEAST v1.5.x branch). (fixed broken build)

4 lines of code changed in 1 file:

rambaut 2010-06-12 03:51 Rev.: 3252

Prettied-up the printing of diagnostic message for a zero initial likelihood (actually this is a port of a improvement from the BEAST v1.5.x branch).

20 lines of code changed in 3 files:

dong.w.xie 2010-06-11 18:47 Rev.: 3251

TRUNK: new tracer dev: user guide.

1 lines of code changed in 2 files:

akaruiws 2010-06-11 17:33 Rev.: 3250

Random index of the bitvector generated by MathUtils.random(n) instead of Math.random.

5 lines of code changed in 2 files:

dong.w.xie 2010-06-11 16:50 Rev.: 3249

TRUNK: new tracer dev: fix remove all filters bug.

110 lines of code changed in 3 files:

akaruiws 2010-06-11 12:47 Rev.: 3248

Msat model averaging.

962 lines of code changed in 13 files:

dong.w.xie 2010-06-11 00:01 Rev.: 3247

TRUNK: new tracer: fixing status message bug after filter applied.

84 lines of code changed in 4 files:

dong.w.xie 2010-06-10 11:43 Rev.: 3246

TRUNK: new tracer dev: finish continuous value filter.

19 lines of code changed in 2 files:

dong.w.xie 2010-06-09 15:51 Rev.: 3245

TRUNK: new tracer dev: add continuous value panel in filter dialog.

42 lines of code changed in 1 file:

dong.w.xie 2010-06-09 15:12 Rev.: 3244

TRUNK: new tracer dev: fix filter plotting bug in all panels.

177 lines of code changed in 7 files:

dong.w.xie 2010-06-09 13:04 Rev.: 3243

TRUNK: new tracer dev: bug fixing again.

138 lines of code changed in 9 files:

dong.w.xie 2010-06-08 16:11 Rev.: 3240

TRUNK: new tracer dev: more bug fixing.

64 lines of code changed in 8 files:

dong.w.xie 2010-06-08 12:26 Rev.: 3239

TRUNK: new tracer dev: add filter status message.

23 lines of code changed in 3 files:

dong.w.xie 2010-06-08 11:36 Rev.: 3238

TRUNK: new tracer dev: fix filter plotting bug for single selected trace only.

68 lines of code changed in 3 files:

rambaut 2010-06-08 04:20 Rev.: 3237

A few tweaks

12 lines of code changed in 4 files:

rambaut 2010-06-07 23:59 Rev.: 3236

Normalized the naming of a few classes and added a note in the MCMC parser to say if the fullEvaluation has been turned off.

361 lines of code changed in 8 files:

rambaut 2010-06-07 23:07 Rev.: 3235

Simplified TreeTrait interface to remove explicit dimensionality. If multidimensional traits are required then it needs to use double[] as the type.

502 lines of code changed in 30 files:

rambaut 2010-06-07 23:04 Rev.: 3234

Reintroduced a loadTraces function with default values. What do reloadColumn and reloadType actually do here?

17 lines of code changed in 1 file:

akaruiws 2010-06-06 22:12 Rev.: 3233

Misc changes to classes for msat likelihood calculation.

308 lines of code changed in 8 files:

jheled 2010-06-06 20:49 Rev.: 3232

Add an option to dump all demographics to a file

33 lines of code changed in 4 files:

jheled 2010-06-06 20:48 Rev.: 3231

Remove annoying debug print

3 lines of code changed in 1 file:

akaruiws 2010-06-06 16:23 Rev.: 3230

Misc changes to msat models.

201 lines of code changed in 8 files:

msuchard 2010-06-06 04:51 Rev.: 3229

Added an ascertainment correction unit test.

255 lines of code changed in 7 files:

msuchard 2010-06-05 10:41 Rev.: 3226

AbstractMultivariateTraitLikelihood can now take a random sample of taxon attributes, in case there are too many (like with genome-wide SNPs)

37 lines of code changed in 1 file:

rambaut 2010-06-05 03:38 Rev.: 3225

Started to get DiscreteTraitRateModel working with dwell time from a MJBTL.

40 lines of code changed in 4 files:

rambaut 2010-06-05 02:18 Rev.: 3224

Fixed TreeTrait to deal with a null trait value array (for example from the root of a tree).

42 lines of code changed in 7 files:

dong.w.xie 2010-06-04 18:19 Rev.: 3223

TRUNK: new tracer dev: try to fix filter bug.

56 lines of code changed in 2 files:

dong.w.xie 2010-06-04 15:56 Rev.: 3222

TRUNK: beauti: more for user-specified starting tree.

25 lines of code changed in 2 files:

dong.w.xie 2010-06-03 11:33 Rev.: 3221

TRUNK: beauti: add function to display user-specified starting tree.

54 lines of code changed in 4 files:

msuchard 2010-06-03 06:20 Rev.: 3220

Fixing bug in dynamic rescaling such that first under-/over-flow triggers a switch over to using scale factors.

17 lines of code changed in 1 file:

rambaut 2010-06-03 01:12 Rev.: 3219

Deleting redundant dr.app.beagle.evomodel.branchratemodel.MarkovJumpsBranchRateModel.

0 lines of code changed in 1 file:

rambaut 2010-06-03 01:10 Rev.: 3218

I have abandoned dr.app.beagle.evomodel.branchratemodel.MarkovJumpsBranchRateModel and integrated that functionality into DiscreteTraitRateModel. This latter class now takes a TreeTrait which is either of the Integer type in which case it is assumed to be a node reconstruction of the state or a 'double[]' type in which case it is assumed to be a vector of dwell times for each state for each branch. I have also left the option of a parsimony reconstruction. I have also restructured things so that everything is done as dwell times - the node reconstruction variants (both likelihood and parsimony) just assume a state transition mid point on the branch. I have tried to average the parsimony variant across ambiguous state reconstructions at the nodes but I am not sure that this is a good idea (but then probably the same could be said for the whole parsimony approximation).

129 lines of code changed in 2 files:

rambaut 2010-06-02 23:13 Rev.: 3217

Fixed a bug in the TreeTraitProvider helper class.

2 lines of code changed in 1 file:

rambaut 2010-06-02 23:10 Rev.: 3216

In the interests of generalization, AncestralState has been improved to optionally take a trait name, renamed AncestralTrait, moved to dr.evomodel.tree. It has a parser synonym of AncestralState and defaults to getting the 'state' trait so it is backwards compatible with existing XML (namely testAncestralSequenceReconstuction.xml).

169 lines of code changed in 5 files:

rambaut 2010-06-02 22:53 Rev.: 3215

TreeTraits commit number 2. This one is a bit more wide ranging with potential to break things. 1) BranchAttributeProvider and NodeAttributeProvider have been deleted and replaced with a combination of TreeTraits and TreeTraitProviders. Sources implement TreeTraitProvider to say that they can provide information about nodes and branches. A good example of a class which has been generalized is AncestralState (in evomodel.treelikelihood) - this now just takes a TreeTrait and logs the trait for a given MRCA (the trait can be anything at all - whereas previously it took an AncestralStateTreeLikelihood).

1160 lines of code changed in 44 files:

dong.w.xie 2010-06-02 15:22 Rev.: 3214

TRUNK: new tracer dev: try to fix filter bug in plot.

30 lines of code changed in 4 files:

dong.w.xie 2010-06-02 10:44 Rev.: 3213

TRUNK: beauti: add newick format starting tree generator.

159 lines of code changed in 5 files:

jheled 2010-06-02 07:05 Rev.: 3212

Allow multiple moves

16 lines of code changed in 1 file:

jheled 2010-06-02 07:04 Rev.: 3211

code police

7 lines of code changed in 10 files:

jheled 2010-06-02 07:04 Rev.: 3210

Allow multiple moves in operator (via a user speciefied 'count')

8 lines of code changed in 1 file:

jheled 2010-06-02 07:02 Rev.: 3209

Make tree height statistic available

48 lines of code changed in 1 file:

jheled 2010-06-02 06:57 Rev.: 3208

Make radius optional, as originally intended

1 lines of code changed in 2 files:

rambaut 2010-06-02 00:12 Rev.: 3207

This update does a number of things. 1) TreeLoggerParser and DemographicLoggerParser were in dr.inferencexml which breaks the dependency rules as they link to things in dr.evomodel. These are now moved to dr.evomodelxml. 2) A dr.evolution.tree.TreeTrait interface is created which is a general purpose interface for access to traits on nodes/branches. BranchAttributeProvider and NodeAttributeProvider will be replaced by this interface in the next update. 3) All BranchRateModels now have a common abstract base class AbstractBranchRateModel to implement their common features (these now implement TreeTrait to provide rates).

882 lines of code changed in 60 files:

rambaut 2010-06-01 20:52 Rev.: 3206

Copied the new all-encompassing GeneralSubstitutionModelParser into dr.app.beagle.parsers to keep BEAST/BEAGLE XML compatibility.

108 lines of code changed in 2 files:

dong.w.xie 2010-06-01 15:22 Rev.: 3205

TRUNK: new tracer dev: add remove all filters.

23 lines of code changed in 2 files:

dong.w.xie 2010-06-01 13:01 Rev.: 3204

TRUNK: new tracer dev merged from branch TRACER_NEW_DEV.

2873 lines of code changed in 52 files:

May 2010 »

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