November 2008 Commit Log

Number of Commits:
78
Number of Active Developers:
8
alexei.drummond 2008-11-29 06:14 Rev.: 1345

Added removeParameter functionality to CompoundParameter to faciliate removal of ARGCompoundParameter and VariableSizeCompoundParameter classes to integrate the ARG code more fully. A small success for simplification against the growing tide of class proliferation!

353 lines of code changed in 10 files:

jheled 2008-11-29 06:00 Rev.: 1344

Remove non supported demographic from Wilson Balding in Beauti

17 lines of code changed in 2 files:

rambaut 2008-11-29 01:37 Rev.: 1343

Fixed issue in EBSPAnalysis where it assumed at least 2 tree files even if single-locus analysis.

9 lines of code changed in 1 file:

alexander.alekseyenko 2008-11-28 06:28 Rev.: 1342

Added implementation of Lewis' Mk Model (cf. Syst. Biol. 50(6):913-925, 2001)

65 lines of code changed in 2 files:

alexander.alekseyenko 2008-11-28 04:33 Rev.: 1341

Massive refactoring of MSSD model specification. See new example file testMSSD.xml to appreciate the resulting simplifications.

377 lines of code changed in 7 files:

alexei.drummond 2008-11-27 21:21 Rev.: 1340

Moved ParameterChangeType -> Parameter.ChangeType

472 lines of code changed in 83 files:

jheled 2008-11-27 15:58 Rev.: 1339

108 lines of code changed in 1 file:

alexei.drummond 2008-11-27 13:22 Rev.: 1338

I reinstated inspectParameterValues method in Parameter.Default rather than the Parameter interface. Interfaces should not have methods that force or expect a certain internal representation. Also, interfaces should be slim! Special hacks designed to increase efficiency should be confined to concrete classes.

17 lines of code changed in 2 files:

alexei.drummond 2008-11-27 13:08 Rev.: 1337

added variable size functionality to Parameter

13725 lines of code changed in 92 files:

jheled 2008-11-27 08:05 Rev.: 1336

Commit initial version of SHE BEAST (temporary name).
Please do not change anything. still work in progress.

1941 lines of code changed in 5 files:

jheled 2008-11-27 08:03 Rev.: 1335

remove printout to stderr - do this only via loggers

1 lines of code changed in 1 file:

jheled 2008-11-27 08:02 Rev.: 1334

code police

20 lines of code changed in 4 files:

msuchard 2008-11-27 05:31 Rev.: 1333

Fixed GMRF Beauti options. Added SubstitutionEpochModel -- allows for different substitution models across time-epochs.

453 lines of code changed in 10 files:

rambaut 2008-11-27 01:44 Rev.: 1332

Have tried to make the connections between the different panels a bit more robust. GetOptions/SetOptions is now called when a new tab is selected. Have fixed a problem with delta exchange on allMus having a weight of 0 and thus not being put into the mix.

670 lines of code changed in 12 files:

jheled 2008-11-26 13:13 Rev.: 1331

Another erronous TreeModel where Tree is sufficient

1 lines of code changed in 1 file:

bloomquist 2008-11-26 08:29 Rev.: 1330

Added a method to MCLogger that stores the fileName.

32 lines of code changed in 2 files:

alexei.drummond 2008-11-25 13:52 Rev.: 1329

removed annoying duplication of log messages during xml parsing

31 lines of code changed in 1 file:

alexander.alekseyenko 2008-11-25 04:43 Rev.: 1328

Fixed store/restore problems whith tree updates in MSSD observation process.

76 lines of code changed in 2 files:

alexander.alekseyenko 2008-11-25 04:40 Rev.: 1327

Minor changes in pathSampling output + updated example.

17 lines of code changed in 2 files:

jheled 2008-11-24 15:22 Rev.: 1326

Comments, nitpicking

36 lines of code changed in 2 files:

rambaut 2008-11-24 12:11 Rev.: 1325

Added a 'DemographicLogger' - this is a logger for recording reconstructions (popsizes + change points) for skyline, skyride type models. The logger takes a class that implements 'DemographicReconstructor' interface. For BSPs this is the BayesianSkylineLikelihood itself.

The actual reconstruction has not been implemented for BSP yet.

Added an Exponential-growth BSP model.

541 lines of code changed in 9 files:

Michael.DefoinPLatel 2008-11-22 00:26 Rev.: 1324

Replace the test file

366 lines of code changed in 1 file:

victor.obolonkin@gmail.com 2008-11-21 09:40 Rev.: 1323

Doesn't crash if log file and tree rates do not match. Matches them and performs the analysis with the warning message.

51 lines of code changed in 1 file:

alexander.alekseyenko 2008-11-21 04:16 Rev.: 1322

Added ascertainment correction to treeLikelihood. If hit with ascertainedSitePatterns it will automagically compute the corrected log-likelihood. see example file.

209 lines of code changed in 2 files:

rambaut 2008-11-20 13:03 Rev.: 1321

Added a piecewise-exponential growth model.

721 lines of code changed in 3 files:

alexei.drummond 2008-11-20 07:43 Rev.: 1320

handling of booleans

53 lines of code changed in 2 files:

Michael.DefoinPLatel 2008-11-20 06:41 Rev.: 1319

I finalize the intergration of the autocorrelated relaxed clock into Beauti. The final user still needs to be clever and check the settings of the priors (maybe some warnings should be added). In addition, I setup a test file for the autocorrelated model. Finally, I released Ziheng Yang's UNcorrelated model for further comparison with Drummond et al 2006 paper (so far I haven't seen any difference between the discretized and continuous version).

211 lines of code changed in 12 files:

jheled 2008-11-19 12:11 Rev.: 1318

Code Police

98 lines of code changed in 42 files:

jheled 2008-11-19 12:09 Rev.: 1317

Add user settable minimum threshold for tree support
Set posterior of root to the mean (in log space, i.e. geometric mean) of clade support. The posterior so far was always 1, so not useful anyway
Generify CladeSet

94 lines of code changed in 4 files:

jheled 2008-11-19 12:08 Rev.: 1316

Return error message (instead of crash) when target tree is empty
Fallback to newick file if file, as nexus, contain no trees.
remove unused argument
code style changes

53 lines of code changed in 2 files:

jheled 2008-11-19 12:05 Rev.: 1315

Added missing space in output

2 lines of code changed in 1 file:

rambaut 2008-11-18 04:44 Rev.: 1314

Fixing up TreeStat v1.2 for release.

187 lines of code changed in 4 files:

jheled 2008-11-17 13:15 Rev.: 1313

Code Police

52 lines of code changed in 5 files:

jheled 2008-11-17 13:14 Rev.: 1312

Generify, add search

23 lines of code changed in 1 file:

jheled 2008-11-17 13:13 Rev.: 1311

Added ability to export trees to nexus file.
Added posterior and height range attributes to exported nodes.

115 lines of code changed in 1 file:

jheled 2008-11-17 13:10 Rev.: 1310

For short analysis, print file name instead of "combined" when ther eis only one file.
Added ability to export trees to nexus file.
Added posterior and height range attributes to exported nodes.

73 lines of code changed in 2 files:

jheled 2008-11-17 13:09 Rev.: 1309

Handle root attributes correctly. (e.g. tree [comment] = [&R] [&W xxx] (( ...))

38 lines of code changed in 2 files:

jheled 2008-11-17 13:08 Rev.: 1308

Export tree weight (MyBayes format [&W xxx]
Export top level attributes (e.g. tree0 [p0 = .2] = [&R] ((...))

33 lines of code changed in 1 file:

msuchard 2008-11-16 12:35 Rev.: 1307

Added operator for Philippe to permute tip-state data. It's not pretty, because there's no store/restore for tip-states, but it works.

128 lines of code changed in 4 files:

rambaut 2008-11-16 00:12 Rev.: 1306

Added a statistic to TreeStat to obtain the mean of an attribute across a clade.

304 lines of code changed in 5 files:

bloomquist 2008-11-15 11:44 Rev.: 1305

Hacked this class for a specific need.

30 lines of code changed in 1 file:

msuchard 2008-11-15 05:04 Rev.: 1304

Fixed null pointer bug in ThreadedCompoundLikelihood. It runs, but with considerably? higher overhead than the Java concurrency methods. Need to tune waits()?

11 lines of code changed in 1 file:

alexander.alekseyenko 2008-11-15 04:27 Rev.: 1303

Added expected identy by descent node reporter.
IBDReporter -- marginal expectation of number of tips identical by descent
AvgPosteriorIBDPeporter -- the same but conditional on sites and averaged over the alignment

1484 lines of code changed in 8 files:

rambaut 2008-11-14 13:47 Rev.: 1302

Added a multithreading CompoundLikelihood. This is for use with GPUs in order to maintain a constant relationship between the threads and the likelihood cores. As such it doesn't use thread pools but a cruder home-brew code.

305 lines of code changed in 2 files:

bloomquist 2008-11-14 10:42 Rev.: 1301

Fixed minor runtime error in timing statistic.

3 lines of code changed in 1 file:

bloomquist 2008-11-14 08:36 Rev.: 1300

Added a log message for the timing statistic.

4 lines of code changed in 1 file:

bloomquist 2008-11-14 08:23 Rev.: 1299

Added statistic to give heights of reassortment events.

93 lines of code changed in 2 files:

jheled 2008-11-13 14:47 Rev.: 1298

Added comment to prevent a future where novices like myself "improve" the code by combining the two loops.

3 lines of code changed in 1 file:

alexander.alekseyenko 2008-11-13 14:00 Rev.: 1297

Added shoe-lacing strategy to path sampling MLE. <marginalLikelihoodEstimator> now takes a 'lacing' attribute to switch this strategy on.

109 lines of code changed in 1 file:

rambaut 2008-11-13 06:46 Rev.: 1296

Fixed an issue with scale operator not scaling all node heights correctly (issue 65)

5 lines of code changed in 1 file:

rambaut 2008-11-11 10:10 Rev.: 1295

Added an upper bound (1000) to gamma shape parameters to match the hard bounds within the code.

5 lines of code changed in 1 file:

rambaut 2008-11-08 12:59 Rev.: 1294

Added single/multi locus option for extended BSP. GUI only at the moment - generation needs to be added for multi-loci.

19 lines of code changed in 3 files:

jheled 2008-11-08 12:57 Rev.: 1293

Comments, nitpicking

15 lines of code changed in 3 files:

jheled 2008-11-08 11:51 Rev.: 1292

Remove non implemented option

3 lines of code changed in 1 file:

jheled 2008-11-08 11:49 Rev.: 1291

Use midpoints by default

4 lines of code changed in 1 file:

jheled 2008-11-07 14:48 Rev.: 1290

Make -heights default explicit in help message
Restore option to send output to stdout
Send progress messages/printout to stderr.
Convert to using enums.
Annotator Dialog takes semantics from Annotator

141 lines of code changed in 2 files:

jheled 2008-11-07 14:44 Rev.: 1289

Overriding Methods can return super types. Change getExternalNode to return SimpleNode

7 lines of code changed in 1 file:

jheled 2008-11-07 14:39 Rev.: 1288

Allow any tree. Restriction of using only a tree model is silly

2 lines of code changed in 1 file:

msuchard 2008-11-07 10:26 Rev.: 1287

Hidden codons run under GPU, substitution model is still a mess

25 lines of code changed in 7 files:

msuchard 2008-11-07 06:25 Rev.: 1286

Hidden codon states are fun!

260 lines of code changed in 7 files:

msuchard 2008-11-06 14:28 Rev.: 1285

Started preparing for multiple partitions on a GPU and multiple GPUs driven in different CPU threads

184 lines of code changed in 2 files:

msuchard 2008-11-06 12:28 Rev.: 1284

GPU initialization no longer spits out NativeLikelihoodCore message

7 lines of code changed in 2 files:

msuchard 2008-11-06 11:06 Rev.: 1283

Added flag to LikelihoodCoreFactory to set precision

6 lines of code changed in 1 file:

rambaut 2008-11-06 10:51 Rev.: 1282

Fixed a couple of build errors

31 lines of code changed in 3 files:

msuchard 2008-11-06 02:16 Rev.: 1281

Restored FGLC which I accidentally deleted previously; may now return results similar to GPU

410 lines of code changed in 2 files:

jheled 2008-11-05 21:30 Rev.: 1280

Fix issue 63

17 lines of code changed in 1 file:

rambaut 2008-11-05 12:01 Rev.: 1279

Started work on an overhaul of SubstitutionModel. This is motivated by newtreelikelihood and the GPU work but is also aiming to simplify the very complex hierarchy in subtmodel. SubstitutionModel is the interface, BaseSubstitutionModel is a base for most models. HKY no longer uses the analytical form. The Eigen system is now provided as a plug in so better methods can be switched in.

1814 lines of code changed in 7 files:

rambaut 2008-11-05 00:09 Rev.: 1278

Reversion

1 lines of code changed in 1 file:

jheled 2008-11-04 20:10

code nitpicking

5 lines of code changed in 3 files:

jheled 2008-11-04 20:09 Rev.: 1275

Allow zero offset by default

2 lines of code changed in 1 file:

jheled 2008-11-04 20:08 Rev.: 1274

code nitpicking

2 lines of code changed in 1 file:

jheled 2008-11-04 20:06 Rev.: 1273

Dimention returned was incorrect in some cases

3 lines of code changed in 1 file:

jheled 2008-11-04 20:04 Rev.: 1272

Force leaf node to have height 0 (numerical instability when reading tree from text)

12 lines of code changed in 1 file:

rambaut 2008-11-04 12:19 Rev.: 1271

Packaged the whole pattern compression algorithm into a LikelihoodCore - this is still a Java version. Some initial testing before deciding whether it is worth doing a native version.

135 lines of code changed in 6 files:

Michael.DefoinPLatel 2008-11-04 04:17 Rev.: 1270

Completed the intergration of the Autocorrelated clock model into Beauti + improvement in the model itself. I am still not happy with the special operators, so they should not be used so far.

554 lines of code changed in 10 files:

rambaut 2008-11-03 05:00 Rev.: 1269

Created an experimental system for compressing site patterns for individual subtrees. At the moment this is entirely implemented in Java. Some profiling will be needed to see if the overhead of the compression is less than the gain in speed. No attempt to optimize the code has been attempted yet.

1745 lines of code changed in 6 files:

rambaut 2008-11-02 12:54 Rev.: 1268

Cleaning up and testing

199 lines of code changed in 10 files:

jheled 2008-11-01 06:13 Rev.: 1267

Remove depracated use of constant demographic in Wilson Balding operator
Merge some uses of the "rootHeight" constant string

1083 lines of code changed in 18 files:

October 2008 »

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