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beast...@googlecode.com

4/24/15

[beast-mcmc] r6756 committed - Update Pybus et al (2012) citation

Revision: 6756 Author: msuchard Date: Fri Apr 24 19:39:23 2015 UTC Log: Update Pybus et al (2012)

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[beast-mcmc] r6756 committed - Update Pybus et al (2012) citation

Revision: 6756 Author: msuchard Date: Fri Apr 24 19:39:23 2015 UTC Log: Update Pybus et al (2012)

4/24/15

beast...@googlecode.com

4/24/15

[beast-mcmc] r6755 committed - Small inconsistency in code

Revision: 6755 Author: msuchard Date: Fri Apr 24 17:40:18 2015 UTC Log: Small inconsistency in code

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[beast-mcmc] r6755 committed - Small inconsistency in code

Revision: 6755 Author: msuchard Date: Fri Apr 24 17:40:18 2015 UTC Log: Small inconsistency in code

4/24/15

beast...@googlecode.com

4/24/15

[beast-mcmc] r6754 committed - Hastings ratio implemented

Revision: 6754 Author: rambaut Date: Fri Apr 24 15:19:15 2015 UTC Log: Hastings ratio implemented

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[beast-mcmc] r6754 committed - Hastings ratio implemented

Revision: 6754 Author: rambaut Date: Fri Apr 24 15:19:15 2015 UTC Log: Hastings ratio implemented

4/24/15

beast...@googlecode.com

4/24/15

[beast-mcmc] r6753 committed - Hastings ratio implemented

Revision: 6753 Author: rambaut Date: Fri Apr 24 14:44:00 2015 UTC Log: Hastings ratio implemented

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[beast-mcmc] r6753 committed - Hastings ratio implemented

Revision: 6753 Author: rambaut Date: Fri Apr 24 14:44:00 2015 UTC Log: Hastings ratio implemented

4/24/15

beast...@googlecode.com

4/24/15

[beast-mcmc] r6752 committed - Make a Gibbs version of SwapParameterOperator

Revision: 6752 Author: msuchard Date: Fri Apr 24 13:21:56 2015 UTC Log: Make a Gibbs version of

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[beast-mcmc] r6752 committed - Make a Gibbs version of SwapParameterOperator

Revision: 6752 Author: msuchard Date: Fri Apr 24 13:21:56 2015 UTC Log: Make a Gibbs version of

4/24/15

beast...@googlecode.com

4/24/15

[beast-mcmc] r6751 committed - SwapParameterOperator throws OperatorException when swap is out-of-bou...

Revision: 6751 Author: msuchard Date: Fri Apr 24 04:15:36 2015 UTC Log: SwapParameterOperator throws

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[beast-mcmc] r6751 committed - SwapParameterOperator throws OperatorException when swap is out-of-bou...

Revision: 6751 Author: msuchard Date: Fri Apr 24 04:15:36 2015 UTC Log: SwapParameterOperator throws

4/24/15

beast...@googlecode.com

4/23/15

[beast-mcmc] r6750 committed - Added parser for SwapParameterOperator

Revision: 6750 Author: msuchard Date: Thu Apr 23 23:25:57 2015 UTC Log: Added parser for

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[beast-mcmc] r6750 committed - Added parser for SwapParameterOperator

Revision: 6750 Author: msuchard Date: Thu Apr 23 23:25:57 2015 UTC Log: Added parser for

4/23/15

beast...@googlecode.com

4/23/15

[beast-mcmc] r6749 committed - Swap all parameter values for tipDate swaps

Revision: 6749 Author: msuchard Date: Thu Apr 23 23:20:13 2015 UTC Log: Swap all parameter values for

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[beast-mcmc] r6749 committed - Swap all parameter values for tipDate swaps

Revision: 6749 Author: msuchard Date: Thu Apr 23 23:20:13 2015 UTC Log: Swap all parameter values for

4/23/15

beast...@googlecode.com

4/23/15

[beast-mcmc] r6748 committed - Fixed the STJO parser

Revision: 6748 Author: rambaut Date: Thu Apr 23 18:51:55 2015 UTC Log: Fixed the STJO parser https://

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[beast-mcmc] r6748 committed - Fixed the STJO parser

Revision: 6748 Author: rambaut Date: Thu Apr 23 18:51:55 2015 UTC Log: Fixed the STJO parser https://

4/23/15

beast...@googlecode.com

4/23/15

[beast-mcmc] r6747 committed - Increased accuracy for log-transformed KDE estimation close to zero.

Revision: 6747 Author: bael...@gmail.com Date: Thu Apr 23 18:24:52 2015 UTC Log: Increased accuracy

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[beast-mcmc] r6747 committed - Increased accuracy for log-transformed KDE estimation close to zero.

Revision: 6747 Author: bael...@gmail.com Date: Thu Apr 23 18:24:52 2015 UTC Log: Increased accuracy

4/23/15

beast...@googlecode.com

4/23/15

[beast-mcmc] r6746 committed - Working towards the correct hastings ratio...

Revision: 6746 Author: rambaut Date: Thu Apr 23 16:26:49 2015 UTC Log: Working towards the correct

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[beast-mcmc] r6746 committed - Working towards the correct hastings ratio...

Revision: 6746 Author: rambaut Date: Thu Apr 23 16:26:49 2015 UTC Log: Working towards the correct

4/23/15

beast...@googlecode.com

4/23/15

[beast-mcmc] r6745 committed - Made SubtreeJump a 'tunable' operator - destination is picked as the i...

Revision: 6745 Author: rambaut Date: Thu Apr 23 15:57:29 2015 UTC Log: Made SubtreeJump a '

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[beast-mcmc] r6745 committed - Made SubtreeJump a 'tunable' operator - destination is picked as the i...

Revision: 6745 Author: rambaut Date: Thu Apr 23 15:57:29 2015 UTC Log: Made SubtreeJump a '

4/23/15

beast...@googlecode.com

4/23/15

[beast-mcmc] r6744 committed - Methods to retrieve source and destination likelihoods from PathLikeli...

Revision: 6744 Author: bael...@gmail.com Date: Thu Apr 23 09:59:33 2015 UTC Log: Methods to

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[beast-mcmc] r6744 committed - Methods to retrieve source and destination likelihoods from PathLikeli...

Revision: 6744 Author: bael...@gmail.com Date: Thu Apr 23 09:59:33 2015 UTC Log: Methods to

4/23/15

beast...@googlecode.com

4/23/15

[beast-mcmc] r6743 committed - Minor change to marginal likelihood estimate when sampling from the pr...

Revision: 6743 Author: bael...@gmail.com Date: Thu Apr 23 09:55:14 2015 UTC Log: Minor change to

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[beast-mcmc] r6743 committed - Minor change to marginal likelihood estimate when sampling from the pr...

Revision: 6743 Author: bael...@gmail.com Date: Thu Apr 23 09:55:14 2015 UTC Log: Minor change to

4/23/15

beast...@googlecode.com

4/23/15

[beast-mcmc] r6742 committed - Print diagnosis during path sampling when initial likelihood is zero.

Revision: 6742 Author: bael...@gmail.com Date: Thu Apr 23 09:52:16 2015 UTC Log: Print diagnosis

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[beast-mcmc] r6742 committed - Print diagnosis during path sampling when initial likelihood is zero.

Revision: 6742 Author: bael...@gmail.com Date: Thu Apr 23 09:52:16 2015 UTC Log: Print diagnosis

4/23/15

beast...@googlecode.com

4/16/15

[beast-mcmc] r6741 committed - Ignore potential infinity problems when using independence samplers.

Revision: 6741 Author: bael...@gmail.com Date: Thu Apr 16 14:46:52 2015 UTC Log: Ignore potential

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[beast-mcmc] r6741 committed - Ignore potential infinity problems when using independence samplers.

Revision: 6741 Author: bael...@gmail.com Date: Thu Apr 16 14:46:52 2015 UTC Log: Ignore potential

4/16/15

beast...@googlecode.com

4/16/15

[beast-mcmc] r6740 committed - Gibbs-disguised operators to sample from gamma and normal distribution...

Revision: 6740 Author: bael...@gmail.com Date: Thu Apr 16 14:37:42 2015 UTC Log: Gibbs-disguised

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[beast-mcmc] r6740 committed - Gibbs-disguised operators to sample from gamma and normal distribution...

Revision: 6740 Author: bael...@gmail.com Date: Thu Apr 16 14:37:42 2015 UTC Log: Gibbs-disguised

4/16/15

beast...@googlecode.com

4/16/15

[beast-mcmc] r6739 committed - Test code for gamma distribution.

Revision: 6739 Author: bael...@gmail.com Date: Thu Apr 16 14:36:12 2015 UTC Log: Test code for

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[beast-mcmc] r6739 committed - Test code for gamma distribution.

Revision: 6739 Author: bael...@gmail.com Date: Thu Apr 16 14:36:12 2015 UTC Log: Test code for

4/16/15

beast...@googlecode.com

4/15/15

[beast-mcmc] r6738 committed - Transmission tree logging fixed

Revision: 6738 Author: mdha...@gmail.com Date: Wed Apr 15 16:48:35 2015 UTC Log: Transmission tree

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[beast-mcmc] r6738 committed - Transmission tree logging fixed

Revision: 6738 Author: mdha...@gmail.com Date: Wed Apr 15 16:48:35 2015 UTC Log: Transmission tree

4/15/15

beast...@googlecode.com

4/15/15

[beast-mcmc] r6737 committed - maybe Compund model is enough

Revision: 6737 Author: fbielejec Date: Wed Apr 15 14:12:08 2015 UTC Log: maybe Compund model is

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[beast-mcmc] r6737 committed - maybe Compund model is enough

Revision: 6737 Author: fbielejec Date: Wed Apr 15 14:12:08 2015 UTC Log: maybe Compund model is

4/15/15

beast...@googlecode.com

4/14/15

[beast-mcmc] r6736 committed - branch model for testing assignments

Revision: 6736 Author: fbielejec Date: Tue Apr 14 13:25:00 2015 UTC Log: branch model for testing

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[beast-mcmc] r6736 committed - branch model for testing assignments

Revision: 6736 Author: fbielejec Date: Tue Apr 14 13:25:00 2015 UTC Log: branch model for testing

4/14/15

beast...@googlecode.com

4/14/15

[beast-mcmc] r6735 committed - Adding working priors for generalized stepping stone sampling.

Revision: 6735 Author: bael...@gmail.com Date: Tue Apr 14 09:33:53 2015 UTC Log: Adding working

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[beast-mcmc] r6735 committed - Adding working priors for generalized stepping stone sampling.

Revision: 6735 Author: bael...@gmail.com Date: Tue Apr 14 09:33:53 2015 UTC Log: Adding working

4/14/15

beast...@googlecode.com

4/14/15

[beast-mcmc] r6734 committed - Adding KDE construction with normal kernels after logit transformation...

Revision: 6734 Author: bael...@gmail.com Date: Tue Apr 14 09:33:03 2015 UTC Log: Adding KDE

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[beast-mcmc] r6734 committed - Adding KDE construction with normal kernels after logit transformation...

Revision: 6734 Author: bael...@gmail.com Date: Tue Apr 14 09:33:03 2015 UTC Log: Adding KDE

4/14/15

beast...@googlecode.com

4/13/15

[beast-mcmc] r6733 committed - Finished test script for log transformed KDE distribution.

Revision: 6733 Author: bael...@gmail.com Date: Mon Apr 13 12:47:30 2015 UTC Log: Finished test

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[beast-mcmc] r6733 committed - Finished test script for log transformed KDE distribution.

Revision: 6733 Author: bael...@gmail.com Date: Mon Apr 13 12:47:30 2015 UTC Log: Finished test

4/13/15

beast...@googlecode.com

4/12/15

[beast-mcmc] r6732 committed - Bug fix

Revision: 6732 Author: mdha...@gmail.com Date: Sun Apr 12 17:02:34 2015 UTC Log: Bug fix https://

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[beast-mcmc] r6732 committed - Bug fix

Revision: 6732 Author: mdha...@gmail.com Date: Sun Apr 12 17:02:34 2015 UTC Log: Bug fix https://

4/12/15

beast...@googlecode.com

4/10/15

[beast-mcmc] r6731 committed - Fix debugging options and add simple test for KDE distribution.

Revision: 6731 Author: bael...@gmail.com Date: Fri Apr 10 12:37:38 2015 UTC Log: Fix debugging

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[beast-mcmc] r6731 committed - Fix debugging options and add simple test for KDE distribution.

Revision: 6731 Author: bael...@gmail.com Date: Fri Apr 10 12:37:38 2015 UTC Log: Fix debugging

4/10/15

beast...@googlecode.com

4/10/15

[beast-mcmc] r6730 committed - Added timing tests and debug option to the KDE distributions.

Revision: 6730 Author: bael...@gmail.com Date: Fri Apr 10 09:27:25 2015 UTC Log: Added timing tests

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[beast-mcmc] r6730 committed - Added timing tests and debug option to the KDE distributions.

Revision: 6730 Author: bael...@gmail.com Date: Fri Apr 10 09:27:25 2015 UTC Log: Added timing tests

4/10/15

beast...@googlecode.com

4/9/15

[beast-mcmc] r6729 committed - Fixed a bug where TT and PT timings were not the same (to 11 decimal p...

Revision: 6729 Author: mdha...@gmail.com Date: Thu Apr 9 12:41:26 2015 UTC Log: Fixed a bug where

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[beast-mcmc] r6729 committed - Fixed a bug where TT and PT timings were not the same (to 11 decimal p...

Revision: 6729 Author: mdha...@gmail.com Date: Thu Apr 9 12:41:26 2015 UTC Log: Fixed a bug where

4/9/15

beast...@googlecode.com

4/9/15

[beast-mcmc] r6728 committed - Added getInverseIntegral for simulation purposes (because getIntensity...

Revision: 6728 Author: mdha...@gmail.com Date: Thu Apr 9 12:40:06 2015 UTC Log: Added

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[beast-mcmc] r6728 committed - Added getInverseIntegral for simulation purposes (because getIntensity...

Revision: 6728 Author: mdha...@gmail.com Date: Thu Apr 9 12:40:06 2015 UTC Log: Added

4/9/15

beast...@googlecode.com

4/7/15

[beast-mcmc] r6727 committed - Transmission tree logging fixed

Revision: 6727 Author: mdha...@gmail.com Date: Tue Apr 7 10:03:54 2015 UTC Log: Transmission tree

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[beast-mcmc] r6727 committed - Transmission tree logging fixed

Revision: 6727 Author: mdha...@gmail.com Date: Tue Apr 7 10:03:54 2015 UTC Log: Transmission tree

4/7/15

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