April 2008 Commit Log

Number of Commits:
37
Number of Active Developers:
6
Michael.DefoinPLatel 2008-04-30 18:33 Rev.: 840

Allow treeTraceAnalysis to check if a reference tree is present in the credible set (using the shortReport mehtod only)

59 lines of code changed in 2 files:

jheled 2008-04-30 14:37 Rev.: 839

Issue 49

1 lines of code changed in 1 file:

Michael.DefoinPLatel 2008-04-30 12:13 Rev.: 838

Extend the model to allow the number of effective categories to be different from the number of branches + bug fix (the rightmost quantile was never used)

26 lines of code changed in 1 file:

Michael.DefoinPLatel 2008-04-30 11:57 Rev.: 837

Bug fix

113 lines of code changed in 1 file:

Michael.DefoinPLatel 2008-04-30 11:56 Rev.: 836

Allow optional upper and lower. If optional then the boundaries are obtained directly from the parameter.

15 lines of code changed in 1 file:

Michael.DefoinPLatel 2008-04-30 11:53 Rev.: 835

Restore TruncNormalDistribution

41 lines of code changed in 1 file:

Michael.DefoinPLatel 2008-04-30 11:51 Rev.: 834

Autocorrelated clock model of rate evolution (Yang and Rannala 2006). This should eventualy replace former RateChangeLikelihood and {ED,GD,LN}Likelihood

364 lines of code changed in 2 files:

msuchard 2008-04-30 00:53 Rev.: 833

T-distributed continuous model stuff

1559 lines of code changed in 17 files:

jheled 2008-04-27 17:42 Rev.: 832

experimental on-the-fly updating of operator weights with -otfops. Absolutly no guarantee - may make things worse

130 lines of code changed in 13 files:

jheled 2008-04-27 09:59 Rev.: 831

experimental Ornstein-Uhlenbeck prior likelihood

196 lines of code changed in 2 files:

jheled 2008-04-26 23:12 Rev.: 830

cosmetics and comment

6 lines of code changed in 1 file:

jheled 2008-04-26 23:11 Rev.: 829

Save data in rows option

45 lines of code changed in 1 file:

jheled 2008-04-26 23:10 Rev.: 828

oops should be with previous bunch

4 lines of code changed in 1 file:

jheled 2008-04-26 23:07 Rev.: 827

fix java generics use

5 lines of code changed in 1 file:

jheled 2008-04-26 23:05 Rev.: 826

fix MIssing attribute rule

1 lines of code changed in 1 file:

jheled 2008-04-26 23:03

Implement log-space for EBSP
Improve loading speed of big trace files and performance of EBSP analysis on large logs

99 lines of code changed in 6 files:

jheled 2008-04-26 22:58 Rev.: 823

Return the proper exception from getDouble

9 lines of code changed in 1 file:

jheled 2008-04-26 18:35 Rev.: 822

don't crash on missing attribute

10 lines of code changed in 1 file:

rambaut 2008-04-26 08:31 Rev.: 821

Added the ability to tell a MonophylyStatistic to ignore certain taxa. This allows us to set up a 'backbone' constraint where taxa of interst are free to move about on the backbone. Compiles and runs but still in the process of testing. To use: put an <ignore>...</ignore> containing the taxa or taxon sets to be ignored.

906 lines of code changed in 2 files:

rambaut 2008-04-25 17:32 Rev.: 820

Fixed a problem where TreeAnnotator wouldn't use a target tree with no branch lengths (i.e., a consensus tree). Will now annotate a (say, PAUP) consensus tree.

1 lines of code changed in 2 files:

msuchard 2008-04-21 04:53 Rev.: 819

Make randomizing branch length in init optional.

26 lines of code changed in 1 file:

msuchard 2008-04-19 09:10 Rev.: 818

Fixed bug in Newton-Raphson algorithm in GMRFSkyrideBlockUpdateOperator so that it actually bails out after maxIterations is reached.
Modified the constructor of GMRFSkyrideLikelihood to make sure that no initial coalescent intervals = 0.

35 lines of code changed in 2 files:

msuchard 2008-04-17 07:00 Rev.: 817

Fixed a bug in the scaled-multivariate normal distribution; should only affect diffusion models

1 lines of code changed in 1 file:

jheled 2008-04-15 06:41 Rev.: 816

fix warning

2 lines of code changed in 1 file:

jheled 2008-04-15 06:39 Rev.: 815

make operator name uniqu

3 lines of code changed in 1 file:

jheled 2008-04-15 06:39 Rev.: 814

Small helper to count lines in code

29 lines of code changed in 1 file:

jheled 2008-04-15 06:38 Rev.: 813

Make operator name uniqu

4 lines of code changed in 3 files:

msuchard 2008-04-14 06:35 Rev.: 812

Fixed a bug in the scaled-multivariate normal distribution; should only affect diffusion models

292 lines of code changed in 4 files:

jheled 2008-04-12 17:47 Rev.: 811

make EBSP functional again after it was broken by recent changes. Some small cleanups as well.

165 lines of code changed in 9 files:

jheled 2008-04-12 08:46 Rev.: 810

Generate a CSV header better suited for importing and handling by code

14 lines of code changed in 1 file:

alexei.drummond 2008-04-10 21:14 Rev.: 809

added geometric mean summary statistic to tracer for traces with all values positive. Should be better point estimate for scale parameters.

290 lines of code changed in 5 files:

msuchard 2008-04-10 18:23 Rev.: 808

Fixed GMRFSkyrideLikelihood so that it is compatiable with Tracer to make pretty pictures.

538 lines of code changed in 3 files:

alexander.alekseyenko 2008-04-07 22:11 Rev.: 806

Reorganized stuff into stochasticdollo.
'als' prefix stands for acquisition-loss-substitution, which is a synonym for multi-state stochastic Dollo. Hope this clarifies any confusion.
Had some trouble committing in the previous revisions...

1006 lines of code changed in 7 files:

alexander.alekseyenko 2008-04-07 21:48 Rev.: 805

Reorganized stuff into stochasticdollo.
'als' prefix stands for acquisition-loss-substitution, which is a synonym for multi-state stochastic Dollo. Hope this clarifies any confusion.

0 lines of code changed in 1 file:

rambaut 2008-04-07 16:59 Rev.: 804

Tweak to NexusImporter to read root node attribute values.

5 lines of code changed in 4 files:

rambaut 2008-04-07 16:39 Rev.: 803

Cleaning up the dependencies a bit more (moved some tree stuff out of SimpleMCMCOperator into a new AbstractTreeOperator) and moved some Alternative Splicing stuff out of dr.inference.prior into a new package dr.evomodel.alternativesplicing (I suggest all of the alternative splicing should go in here).

693 lines of code changed in 13 files:

rambaut 2008-04-01 00:53 Rev.: 799

Fixes for the Exponential-Logistic

2 lines of code changed in 2 files:

March 2008 »

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