July 2011 Commit Log

Number of Commits:
63
Number of Active Developers:
8
rambaut 2011-07-31 19:44 Rev.: 4147

Seem to have got the Antigenic MDS working correctly with threshold assay values and replicate measurements.

78 lines of code changed in 1 file:

rambaut 2011-07-31 11:53 Rev.: 4146

Seem to have got the Antigenic MDS working correctly with threshold assay values and replicate measurements.

170 lines of code changed in 3 files:

rambaut 2011-07-30 03:57 Rev.: 4145

Slowly beating this code into shape

154 lines of code changed in 2 files:

msuchard 2011-07-30 03:51 Rev.: 4144

Fixed shrinkage issue when variance is too low

5 lines of code changed in 1 file:

rambaut 2011-07-29 21:36

Test

2 lines of code changed in 2 files:

rambaut 2011-07-29 21:32 Rev.: 4141

Updated ANT script to use new commons maths lib.

2 lines of code changed in 1 file:

rambaut 2011-07-29 20:25 Rev.: 4140

Updating version info

0 lines of code changed in 1 file:

fbielejec 2011-07-29 11:37 Rev.: 4139

added robust counting analysis

31 lines of code changed in 1 file:

fbielejec 2011-07-29 11:35

added flag setter

89 lines of code changed in 2 files:

alexei.drummond 2011-07-29 08:51 Rev.: 4136

added Beta Diversity statistic to Tree Stat

27 lines of code changed in 3 files:

alexei.drummond 2011-07-29 08:07 Rev.: 4135

added Beta Diversity statistic to Tree Stat

175 lines of code changed in 2 files:

rambaut 2011-07-29 05:21 Rev.: 4134

Fixed issue with CTMC Reference prior finding the correct tree model to use.

33 lines of code changed in 2 files:

rambaut 2011-07-29 05:20 Rev.: 4133

Cleaned up selection of tree priors available for different situations.

34 lines of code changed in 4 files:

rambaut 2011-07-29 02:16 Rev.: 4132

Resuming work on this...

3 lines of code changed in 1 file:

rambaut 2011-07-28 11:42 Rev.: 4131

An approximation to the tail of a normal distribution added. To be tested...

73 lines of code changed in 1 file:

rambaut 2011-07-28 11:42 Rev.: 4130

Removed CTMC reference prior checkbox from clock model table (you select this in the improved prior dialog). Also moved note about this in tooltip for this checkbox to a text area that appears in the PriorDialog when this prior is selected.

16 lines of code changed in 4 files:

rambaut 2011-07-28 11:40 Rev.: 4129

Fixed issue with 0 taxa in data table for traits - now shows '-' to denote that it isn't an alignment.

5 lines of code changed in 3 files:

rambaut 2011-07-28 04:08 Rev.: 4128

Addressed issue 472: http://code.google.com/p/beast-mcmc/issues/detail?id=472

Doesn't show operator performance suggestion when auto-optimize is on.

11 lines of code changed in 1 file:

rambaut 2011-07-28 03:39 Rev.: 4127

Added check box when creating a new trait to automatically create the corresponding trait partition. This is on by default.

19 lines of code changed in 3 files:

rambaut 2011-07-28 02:48 Rev.: 4126

-beagle_scaling command line flag turns on BEAGLE in the absence of any other flags.

2 lines of code changed in 1 file:

rambaut 2011-07-28 02:40 Rev.: 4125

Fix for issue 464: http://code.google.com/p/beast-mcmc/issues/detail?id=464

Set the default locale to US at the beginning of the main() of each of the applications. We don't currently do any localization and the use of a comma as a decimal in some places but not other for those languages that use this was causing major incompatibilities.

44 lines of code changed in 11 files:

rambaut 2011-07-28 00:04 Rev.: 4124

Fix for issue 468: http://code.google.com/p/beast-mcmc/issues/detail?id=468

2 lines of code changed in 1 file:

rambaut 2011-07-27 23:43 Rev.: 4123

Removed commons-maths-2.0.jar from lib folder

160 lines of code changed in 2 files:

rambaut 2011-07-27 22:39 Rev.: 4122

Fixed issue 471: http://code.google.com/p/beast-mcmc/issues/detail?id=471

11 lines of code changed in 1 file:

dong.w.xie 2011-07-26 18:42 Rev.: 4121

few correction for starbeast tutorial

529 lines of code changed in 2 files:

rambaut 2011-07-26 04:12 Rev.: 4120

Cleaned up the hierarchical prior button (disabled until a parameter is selected etc).

27 lines of code changed in 1 file:

rambaut 2011-07-26 03:18 Rev.: 4119

TruncatedDistribution more robustly handles quantiles.

41 lines of code changed in 3 files:

rambaut 2011-07-24 06:42 Rev.: 4118

Reverted most of the functions of GammaDistributionModel to use the GD in dr.math. Only the quantile function uses the Commons Math version (to minimize disturbance).

3 lines of code changed in 2 files:

rambaut 2011-07-24 06:30 Rev.: 4117

Switched GammaDistributionModel to use Common Math version to see if that has better numerical stability. Also updated commons-math to the latest version.

14 lines of code changed in 2 files:

rambaut 2011-07-23 04:00 Rev.: 4116

uncommitting an erroneous revision

285 lines of code changed in 44 files:

rambaut 2011-07-22 08:49 Rev.: 4115

Added a UI for BEAST on GUI platforms. Not completely linked yet.

147 lines of code changed in 5 files:

msuchard 2011-07-21 03:39 Rev.: 4114

Removed warning, as reported on beast-users

1 lines of code changed in 2 files:

dong.w.xie 2011-07-19 15:39 Rev.: 4113

update

151 lines of code changed in 3 files:

jheled@gmail.com 2011-07-19 11:47 Rev.: 4112

Add an alternative exact marginal

112 lines of code changed in 4 files:

rambaut 2011-07-16 01:40 Rev.: 4111

Generalized TruncatedDistribution that wraps another distribution. Quantile functions are not robust.

11 lines of code changed in 1 file:

dong.w.xie 2011-07-15 17:17 Rev.: 4110

update my tool after bdss changed

43 lines of code changed in 1 file:

sibon.li 2011-07-15 12:41 Rev.: 4109

Created an app - GetAncestralSequenceFromSplitTrait, which does just that.

347 lines of code changed in 3 files:

dong.w.xie 2011-07-14 16:44 Rev.: 4108

update my tool after bdss changed

4 lines of code changed in 1 file:

rambaut 2011-07-12 23:01 Rev.: 4107

Fixed an issue with JumpHistoryAnalyser not printing results.

15 lines of code changed in 2 files:

dong.w.xie 2011-07-12 18:19 Rev.: 4106

update my tool after bdss changed

15 lines of code changed in 1 file:

dong.w.xie 2011-07-12 11:46 Rev.: 4105

testEBSP.xml, but ess not good

0 lines of code changed in 1 file:

dong.w.xie 2011-07-08 14:53 Rev.: 4104

update my tool since BDSS changed

36 lines of code changed in 1 file:

dong.w.xie 2011-07-08 11:24 Rev.: 4103

comment out system print in BDSS

1 lines of code changed in 1 file:

dong.w.xie 2011-07-07 17:02 Rev.: 4102

GF81

170 lines of code changed in 3 files:

dong.w.xie 2011-07-07 11:29 Rev.: 4101

Trunk: fix BEAUti BDSS part

22 lines of code changed in 3 files:

alexei.drummond 2011-07-06 13:39 Rev.: 4100

parser fix

4 lines of code changed in 2 files:

dong.w.xie 2011-07-04 15:14 Rev.: 4099

Trunk: add xml to compare BEAST 2

241 lines of code changed in 1 file:

jheled@gmail.com 2011-07-04 13:40 Rev.: 4098

more fixes to calibration code

37 lines of code changed in 5 files:

jheled@gmail.com 2011-07-04 13:39 Rev.: 4097

species tree taxa references in XML work now

2 lines of code changed in 1 file:

dong.w.xie 2011-07-04 11:59

Trunk: update xml to compare BEAST 2

11 lines of code changed in 3 files:

fbielejec 2011-07-02 12:37 Rev.: 4094

working on reflection based method overriding default setting

45 lines of code changed in 1 file:

alexei.drummond 2011-07-02 08:48 Rev.: 4093

Tidied up parsers and added option to specify epoch widths from the origin rather than the tips.

61 lines of code changed in 5 files:

fbielejec 2011-07-01 21:54 Rev.: 4092

fix for quotation marks

2 lines of code changed in 1 file:

fbielejec 2011-07-01 21:43 Rev.: 4091

added default tags

159 lines of code changed in 1 file:

dong.w.xie 2011-07-01 15:47 Rev.: 4090

TRUNK: fix Hudson due to change of BDSS

3 lines of code changed in 1 file:

msuchard 2011-07-01 15:37 Rev.: 4089

Connecting DnDsComponent into BEAUti GUI button

75 lines of code changed in 4 files:

dong.w.xie 2011-07-01 14:26 Rev.: 4088

TRUNK: update xmls to compare BEAST 2 results

0 lines of code changed in 3 files:

mandevsgill 2011-07-01 12:09 Rev.: 4087

Now the multilocus Skyride model should work.

5 lines of code changed in 3 files:

mandevsgill 2011-07-01 10:39 Rev.: 4086

Multilocus GMRF model has been updated and appears to be working properly. Old GMRF model should still work with the old xml syntax.

832 lines of code changed in 6 files:

alexei.drummond 2011-07-01 06:56 Rev.: 4085

likelihoods correct! phew! Late night debugging with Denise and Tanja in Zurich ;-)

308 lines of code changed in 3 files:

rambaut 2011-07-01 04:13 Rev.: 4084

Fixing some issues with row/column indexing in the sparse matrix

18 lines of code changed in 2 files:

fbielejec 2011-07-01 03:15 Rev.: 4083

robust dNdS counting classes

171 lines of code changed in 3 files:

fbielejec 2011-07-01 01:29 Rev.: 4082

added DnDs counting button

526 lines of code changed in 1 file:

June 2011 »

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