April 2010 Commit Log

Number of Commits:
36
Number of Active Developers:
5
rambaut 2010-04-29 22:05 Rev.: 3145

Made a change to how BEAUti generates multidimensional parameters: A multidimensional parameter only needs to give initial values for every dimension if they are actually different. A single value will automatically be expanded to every dimension and make for a cleaner looking XML (and more robust to changes in the number of groups/taxa etc.

8 lines of code changed in 1 file:

rambaut 2010-04-29 02:53 Rev.: 3143

Fixed an issue with BEAUti importing calendar dates from an existing XML file. The way the date was converted (using the birthdate of the well-known offspring of a polular deity) was inducing precision problems resulting in inaccurate dates expressed as decimal years (in the order of a month).

28 lines of code changed in 4 files:

msuchard 2010-04-28 12:52 Rev.: 3141

Fixed bug when simulating sequences under general data type

3 lines of code changed in 1 file:

rambaut 2010-04-28 02:36 Rev.: 3140

Added ability to skip trees in the input file to handle memory issues. Also will compute SDR for latitude only.

38 lines of code changed in 1 file:

msuchard 2010-04-25 02:46 Rev.: 3135

CPU-BEAGLE auto-scaling is now working with BEAST; still needs major benchmarking vis-a-vis BEAST's dynamic scaling

8 lines of code changed in 1 file:

msuchard 2010-04-24 13:19 Rev.: 3134

Store/restore with auto-scaling is still not quite working

24 lines of code changed in 3 files:

msuchard 2010-04-24 10:23 Rev.: 3133

Making default scaling in BEAGLE = none, until auto-scaling implementation is working well

3 lines of code changed in 1 file:

msuchard 2010-04-24 06:58 Rev.: 3132

MarkovJumpsBeagleTreeLikelihood now supports all CTMC that can be uniformized (I believe this is all finite-state models).

307 lines of code changed in 8 files:

rambaut 2010-04-23 22:30 Rev.: 3131

More work on the hypermutation model.

182 lines of code changed in 11 files:

rambaut 2010-04-22 23:12 Rev.: 3130

Created an HypermutantAlignment that flags hypermutation contexts for use in the APOBECErrorModel. It does this by replacing 'A's by an ambiguity code for A/G if it is in the correct context in the alignment. These can then be compressed into unique site patterns so that speed is not affected.

Extracted a common abstract base class with ConvertAlignment which wraps an alignment.

867 lines of code changed in 10 files:

philippe.lemey@gmail.com 2010-04-17 19:01 Rev.: 3125

adding continuous phylogeography xml examples

3023 lines of code changed in 4 files:

dong.w.xie 2010-04-16 15:10 Rev.: 3124

TRUNK: modification of Discrete Trait in BEAUti, and change default prior of all clock rates into Gamma(0.001, 1000)

103 lines of code changed in 16 files:

dong.w.xie 2010-04-15 13:23 Rev.: 3123

TRUNK: sovle Issue 296: The imported data has become global to all BEAUti windows

197 lines of code changed in 24 files:

rambaut 2010-04-15 08:40 Rev.: 3122

Minor tweaks to APOBEC model.

47 lines of code changed in 4 files:

dong.w.xie 2010-04-14 14:09 Rev.: 3121

TRUNK: delete SnAPhyl from Trunk

0 lines of code changed in 19 files:

dong.w.xie 2010-04-14 14:03 Rev.: 3119

BRANCH: move SnAPhyl into branch 1.5

20 lines of code changed in 6 files:

alexei.drummond 2010-04-13 18:55 Rev.: 3118

Added an (command-line) option in TreeAnnotator to force integer attributes to be treated as discrete attributes.

22 lines of code changed in 1 file:

dong.w.xie 2010-04-13 18:04 Rev.: 3117

TRUNK: sovle Issue 300: have a single parser 'generalSubstitutionModel' and get rid of 'svsGeneralSubstitutionModel' paser

189 lines of code changed in 12 files:

alexei.drummond 2010-04-13 17:29 Rev.: 3116

Small fixes to migrate conversion program

48 lines of code changed in 4 files:

alexei.drummond 2010-04-13 12:10 Rev.: 3115

Converter for Migrate trees that converts migrations to population reconstructions at internal nodes

456 lines of code changed in 7 files:

dong.w.xie 2010-04-13 11:45 Rev.: 3114

TRUNK: sovle Issue 299: GeneralDataType should be registered for the purpose that DataType.getRegisteredDataTypeNames() returns the correct set of DataType

2 lines of code changed in 2 files:

rambaut 2010-04-13 11:03 Rev.: 3113

Added a few models of sequence (tip) error to model the action of hypermutation by APOBEC editing in HIV.

228 lines of code changed in 9 files:

dong.w.xie 2010-04-12 11:12 Rev.: 3112

TRUNK: sovle Issue 295: If no BSSVS then no need for the indicators parameter

2 lines of code changed in 1 file:

dong.w.xie 2010-04-09 17:56 Rev.: 3111

TRUNK: merge Issue 294 from branch

2 lines of code changed in 1 file:

dong.w.xie 2010-04-09 10:58 Rev.: 3108

TRUNK: BEAUti Discrete Traits: finish initial dev.

56 lines of code changed in 3 files:

msuchard 2010-04-09 07:25 Rev.: 3107

More Fixes to store/restore in ALSTreeLikelihood

68 lines of code changed in 3 files:

dong.w.xie 2010-04-08 19:07 Rev.: 3106

TRUNK: BEAUti Discrete Traits: start gerenrator log.

8 lines of code changed in 2 files:

msuchard 2010-04-08 13:45 Rev.: 3105

Fixed store/restore in ALSTreeLikelihood

30 lines of code changed in 3 files:

msuchard 2010-04-08 13:03 Rev.: 3104

Optimizing stochastic Dollo model; should run 2 - 3x faster now

115 lines of code changed in 3 files:

dong.w.xie 2010-04-08 11:43 Rev.: 3102

TRUNK: BEAUti Discrete Traits: keep going on generator.

87 lines of code changed in 5 files:

msuchard 2010-04-08 11:12 Rev.: 3101

Intermediate fixed to stochastic Dollo; more to follow

41 lines of code changed in 1 file:

dong.w.xie 2010-04-07 17:24 Rev.: 3100

TRUNK: BEAUti Discrete Traits: working on generator, but there is still bugs.

20 lines of code changed in 4 files:

dong.w.xie 2010-04-07 10:11 Rev.: 3099

TRUNK: update primates finally

0 lines of code changed in 1 file:

dong.w.xie 2010-04-07 10:10

TRUNK: try to update primates, it seems my intellij is being funny.

0 lines of code changed in 2 files:

dong.w.xie 2010-04-01 15:23 Rev.: 3096

TRUNK: update primates data.

46 lines of code changed in 2 files:

dong.w.xie 2010-04-01 10:20 Rev.: 3095

TRUNK: merge Issue 291 from branch 1.5.

40 lines of code changed in 2 files:

March 2010 »

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