Directory src/dr/util/

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Most Recent Commits

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

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

1 lines of code changed in 2 files:

• src/dr/util: Transform.java (+1 -1)

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

Fixed transform; they were missing Jacobians in computing densities.

58 lines of code changed in 1 file:

• src/dr/util: Transform.java (+58 -12)

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

Fixed log determinate for large diagonal matrices; refactored transforms.

114 lines of code changed in 1 file:

• src/dr/util: Transform.java (+114 -4)

graham853@gmail.com 2012-09-02 04:49 Rev.: 5149

Allopolyploid model: adding code for arbitrary numbers of diploids, tetraploids, hybridizations.

15 lines of code changed in 2 files:

• src/dr/util: AlloppMisc.java (+15 -17)

graham853@gmail.com 2012-05-10 00:51 Rev.: 4946

Extending allopolyploid model to deal with arbitrary numbers of diploids. Most new code is in new class AlloppDiploidHistory and old class AlloppNetworkNodeSlide.

60 lines of code changed in 1 file:

• src/dr/util: AlloppMisc.java (+60)

rambaut 2012-03-08 04:37 Rev.: 4783

Initial, horribly slow, inefficient re-write of antigenic likelihood.

92 lines of code changed in 2 files:

• src/dr/util: DataTable.java (new)

graham853@gmail.com 2012-01-23 01:15 Rev.: 4600

Improved MCMC moves for allopolyploid model (diploid root, moves of legs).

17 lines of code changed in 1 file:

• src/dr/util: AlloppMisc.java (+17 -1)

rambaut 2012-01-04 02:27 Rev.: 4569

Implemented saving and loading of 'BEAUti' files using Java Serialization. Seems to work but complex models are not yet tested.

10 lines of code changed in 8 files:

• src/dr/util: Attributable.java (new), Attribute.java (new), Identifiable.java (+3 -1), NumberFormatter.java (+2 -1)

rambaut 2011-11-15 05:14 Rev.: 4423

Added citations to amino acid models and a text box in BEAUti.

4 lines of code changed in 2 files:

• src/dr/util: Citation.java (new)

msuchard 2011-09-21 22:54 Rev.: 4329

Fixed store/restore in WeightedMixtureModel

8 lines of code changed in 2 files:

• src/dr/util: CommonCitations.java (new)

rambaut 2011-09-08 11:10 Rev.: 4289

Started to implement continuous traits in BEAUti. Needed extensive cleaning up and streamlining of code.

5 lines of code changed in 1 file:

• src/dr/util: DataTable.java (+5 -3)

graham853@gmail.com 2011-09-02 00:01 Rev.: 4277

66 lines of code changed in 1 file:

• src/dr/util: AlloppMisc.java (+66)

msuchard 2011-08-24 12:38 Rev.: 4238

Latent liability model appears to work well.

8 lines of code changed in 1 file:

• src/dr/util: CommonCitations.java (+8)

msuchard 2011-06-16 07:58 Rev.: 4030

Extended complete histories for multiple sites

27 lines of code changed in 1 file:

• src/dr/util: CommonCitations.java (+27 -1)

msuchard 2011-06-16 04:29 Rev.: 4028

Adding TreeAnnonator parsing ability for MarkovJumps processes with multiple sites. To be used in Markov-modulated substitution models with Chris Simon.

9 lines of code changed in 1 file:

• src/dr/util: CommonCitations.java (+9 -1)

msuchard 2011-03-03 05:44 Rev.: 3847

Add functionality to read plink SNP frequencies and run continuous diffusion models

4 lines of code changed in 1 file:

• src/dr/util: CommonCitations.java (+4 -1)

rambaut 2011-02-07 23:33 Rev.: 3790

More work on AntigenicTraitLikelihood to allow for multiple measurements per antisera

106 lines of code changed in 1 file:

• src/dr/util: DataTable.java (+106 -1)

rambaut 2010-11-13 08:33 Rev.: 3714

AntigenicTraitLikelihood runs! Unlikely to work though. Changed MatrixParameter to set dimensions lazily. TreeTraitParserUtility now labels the individual rows of the compound parameter just as taxon labels so that ATL can pick them up.

11 lines of code changed in 1 file:

• src/dr/util: DataTable.java (+11 -5)

rambaut 2010-11-05 21:56 Rev.: 3700

Added utility class for reading and handling tabular data and applied it to loading an HI table.

132 lines of code changed in 1 file:

• src/dr/util: DataTable.java (+132)

rambaut 2010-08-25 00:37 Rev.: 3434

Strange use of some private Sun API to obtain a line separator caused compile warnings. Changed to System.getProperty("line.separator"). If there was some reason for the previous technique it should have been commented.

10 lines of code changed in 4 files:

• src/dr/util: ErrorLogHandler.java (+5 -2), MessageLogHandler.java (new)

rambaut 2010-08-20 04:13 Rev.: 3414

Added command line option '-prefix <PREFIX>' to specify a string which will be prefixed to all output log files. This is an alternative to changing the log file names in the XML when running multiple replicate runs in the same location.

9 lines of code changed in 2 files:

• src/dr/util: FileHelpers.java (new)

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

TRUNK: new tracer dev merged from branch TRACER_NEW_DEV.

12 lines of code changed in 2 files:

• src/dr/util: FrequencyDistribution.java (new)

msuchard 2010-05-28 07:23 Rev.: 3194

Fixed bug in ascertainment correction (miscounted) and implemented in BEAGLE. Genomic-wide SNPs here we come!

14 lines of code changed in 1 file:

• src/dr/util: CommonCitations.java (+14)

msuchard 2010-02-27 09:30 Rev.: 2990

(1) More testing of robust counting; (2) more work on a citation framework

37 lines of code changed in 1 file:

• src/dr/util: CommonCitations.java (+37)

msuchard 2010-02-20 08:07 Rev.: 2951

Testing different scalings in multivariate trait model

0 lines of code changed in 2 files:

• src/dr/util: Citable.java (-2)

msuchard 2010-02-20 06:15 Rev.: 2950

Continuing work on a unified citation mechanism

144 lines of code changed in 3 files:

• src/dr/util: Author.java (new 27), Citable.java (+43), Citation.java (+74 -9)

dong.w.xie 2009-12-10 16:25 Rev.: 2689

Trunk: merge from branch 1.5 in

5 lines of code changed in 1 file:

• src/dr/util: ErrorLogHandler.java (+5 -1)

alexander.alekseyenko 2009-10-23 02:57 Rev.: 2449

added parsers for Lewis' Mk model with totaly ordered/unordered/custom ordered states.

46 lines of code changed in 1 file:

• src/dr/util: ErrorLogHandler.java (+46 -42)

alexei.drummond 2009-09-24 17:27 Rev.: 2295

55 lines of code changed in 1 file:

• src/dr/util: Citation.java (+55)

dong.w.xie 2009-09-22 15:34 Rev.: 2267

BEAUTi:
1) part of code for Issue 171: Version update reminder in BEAUTi;
2) remove all "/" in the end of URL, which cause error for Wiki.

2 lines of code changed in 2 files:

• src/dr/util: Version.java (+2)

jheled 2009-09-08 11:29 Rev.: 2224

generify via auto intelliJ

2 lines of code changed in 1 file:

• src/dr/util: Attributable.java (+2 -2)

jheled 2009-09-07 08:16 Rev.: 2207

comments changes

10 lines of code changed in 4 files:

• src/dr/util: FileHelpers.java (+1 -1), TabularData.java (new), Transform.java (+2)

jheled 2009-09-07 08:15 Rev.: 2206

automatic intelliJ transforms

5 lines of code changed in 3 files:

• src/dr/util: HeapSort.java (new), MessageLogHandler.java (+3 -4)

jheled 2009-09-07 08:15 Rev.: 2205

code police

5 lines of code changed in 4 files:

• src/dr/util: Attribute.java (+2 -3), ComparableDouble.java (+3 -3), Identifiable.java (-1)

jheled 2009-09-07 08:12

comment out unused code

85 lines of code changed in 4 files:

• src/dr/util: Assert.java (new), CollectionHash.java (new)

jheled 2009-08-06 08:22 Rev.: 2029

intellij auto

1 lines of code changed in 1 file:

• src/dr/util: ErrorLogHandler.java (+1 -1)

rambaut 2009-08-01 23:49 Rev.: 1992

Updated the credits for the upcoming release of BEAST. Note the list of developers in 'BeastVersion.java' is not complete. Please review and revise.

4 lines of code changed in 1 file:

• src/dr/util: Version.java (+4)

alexei.drummond 2009-07-17 01:13 Rev.: 1863

Beginning of refactoring to remove dr.inference.* dependency on dr.xml. Will take a while...

25 lines of code changed in 1 file:

• src/dr/util: FileHelpers.java (+25 -1)

alexei.drummond 2009-07-15 16:25 Rev.: 1860

refactoring to remove illegal dependencies (dr.inference should not depend on dr.evo*.*) and tidying

48 lines of code changed in 1 file:

• src/dr/util: FileHelpers.java (+48)

alexei.drummond 2009-07-13 23:44 Rev.: 1848

Refactoring tidy up. Reducing interdependencies between top-level packages. Will upload dependency guidelines to wiki soon.

409 lines of code changed in 3 files:

• src/dr/util: HeapSort.java (+394 -398), Identifiable.java (+15 -18), Variate.java (del)

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