January 2007 Commit Log

Number of Commits:
31
Number of Active Developers:
4
alexei.drummond 2007-01-30 13:17 Rev.: 182

added BEAST paper in LaTeX format...

636 lines of code changed in 1 file:

jheled 2007-01-26 12:08 Rev.: 175

enable selecting monoph checkbox

5 lines of code changed in 1 file:

jheled 2007-01-26 11:41 Rev.: 174

add monophyly prior support in beauti and beast. (can't check checkbox yet)

223 lines of code changed in 7 files:

jheled 2007-01-25 10:36 Rev.: 172

comments & cosmetic changes

952 lines of code changed in 28 files:

rambaut 2007-01-23 03:54 Rev.: 161

Modification as a result of issue 11. The chain now stops once it has had 10 (definable as a constant in MarkovChain.java) errors. This is so that people don't fail to notice that the state was not restoring properly which seems to happen for certain datasets on certain x86 processors (or perhaps just Linux) when using the native library.

9 lines of code changed in 1 file:

rambaut 2007-01-23 03:39 Rev.: 159

Fixed issue 6 (unable to set number of skyline groups properly)

1 lines of code changed in 1 file:

rambaut 2007-01-23 03:32 Rev.: 157

Fixed issue 5 (guessing dates with prefix)

294 lines of code changed in 5 files:

alexei.drummond 2007-01-22 22:09

72 lines of code changed in 3 files:

msuchard 2007-01-20 13:54 Rev.: 153

ML calculations occur in trace.MarginalLikelihoodAnalysis, extra class removed

0 lines of code changed in 1 file:

jheled 2007-01-19 07:48 Rev.: 150

change units type to an enum
Allow a log file name to be relative to main beast xml file when prefixed with a ./
minor jdoc and 1.5 cleanup

743 lines of code changed in 88 files:

msuchard 2007-01-19 07:35 Rev.: 149

0 lines of code changed in 2 files:

msuchard 2007-01-19 07:35 Rev.: 148

Added a marginal likelihood analysis tool (MarginalLikelihoodAnalysis) to estimate marginal likelihoods using the two methods proposed in Newton and Raftery 1996. testMLCalculator.xml shows how to use the XML constructor.

621 lines of code changed in 5 files:

msuchard 2007-01-19 04:40 Rev.: 147

Starting MarginalLikelihoodAnalysis to estimate marginal likelihoods from a Trace

118 lines of code changed in 1 file:

msuchard 2007-01-18 10:33 Rev.: 145

Removing dependence on numericalMethods.jar in GLM

111 lines of code changed in 3 files:

msuchard 2007-01-18 10:19 Rev.: 143

Added the beginnings of marginal likelihood calculator

0 lines of code changed in 1 file:

jheled 2007-01-18 09:33 Rev.: 141

use randomLogDouble

2 lines of code changed in 1 file:

jheled 2007-01-18 09:25 Rev.: 140

fix incorrect hastings ratio

8 lines of code changed in 1 file:

jheled 2007-01-18 09:17 Rev.: 139

add randomLogDouble. jdoc comments.

37 lines of code changed in 1 file:

jheled 2007-01-18 08:56 Rev.: 138

comments (and first commit test)

6 lines of code changed in 1 file:

alexei.drummond 2007-01-16 11:37

Added a mixed distribution class that uses a different distribution for each element in a statistic based on a second indicator vector

34 lines of code changed in 5 files:

alexei.drummond 2007-01-14 12:32 Rev.: 132

Added a mixed distribution class that uses a different distribution for each element in a statistic based on a second indicator vector

135 lines of code changed in 2 files:

alexei.drummond 2007-01-14 09:33 Rev.: 131

A preliminary version of a new skyline plot that chooses the appropriate number steps automatically using a similar technique to the random local clock model recently added.

9 lines of code changed in 2 files:

alexei.drummond 2007-01-14 00:04 Rev.: 129

A preliminary version of a new skyline plot that chooses the appropriate number steps automatically using a similar technique to the random local clock model recently added.

299 lines of code changed in 1 file:

msuchard 2007-01-13 18:27 Rev.: 128

Removed dependence on numericalMethods.jar.

172 lines of code changed in 3 files:

msuchard 2007-01-13 18:26 Rev.: 127

Removed dependence on numericalMethods.jar. Added Cholesky decomposition class.

63 lines of code changed in 1 file:

alexei.drummond 2007-01-12 13:50 Rev.: 125

added CovarionSubstitutionModel to BeastParser

128 lines of code changed in 1 file:

msuchard 2007-01-05 06:47 Rev.: 122

218 lines of code changed in 2 files:

msuchard 2007-01-03 11:11 Rev.: 121

Converted GeneralizedLinearModel into an abstract class for implementing different linear models. LogisticRegression provides support for the logistic family of GLMs.

62 lines of code changed in 2 files:

msuchard 2007-01-03 10:32 Rev.: 120

The multivariate normal driver requires a Cholesky decomposition. I plugged the decomposition from numericalMethods.jar . Ultimately a stand-alone decomposer needs to be added to BEAST

130 lines of code changed in 2 files:

msuchard 2007-01-03 10:23 Rev.: 119

Added a Generalized Linear Model (GLM) likelihood and a multivariate normal random walk operator. Included are also two classes to specify design matrices when performing regression.

782 lines of code changed in 5 files:

alexei.drummond 2007-01-02 17:41 Rev.: 118

improved log analyzer to output full (relative) file names and to allow the short report to optionally include hpds

30 lines of code changed in 3 files:

December 2006 »

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