May 2010 Commit Log

Number of Commits:
31
Number of Active Developers:
5
philippe.lemey@gmail.com 2010-05-31 22:04 Rev.: 3203

more DnDsPerSiteAnalysis debugging

35 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-05-31 22:03 Rev.: 3202

adding DnDsPerSiteAnalysis parser to development parser list

4 lines of code changed in 1 file:

dong.w.xie 2010-05-31 15:25 Rev.: 3201

TRUNK: follow-up Issue 310 to include beagle.jar in beast.jar for 1.6.0 pre.

4 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-05-31 07:45 Rev.: 3199

debugging DnDsPerSiteAnalysis

32 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-05-30 23:12 Rev.: 3198

adding a trace analysis for N and S counts

269 lines of code changed in 1 file:

msuchard 2010-05-29 08:37 Rev.: 3197

Two goals acheived. (1) RobustCounting now provides per site counts to a log file and (2) example of using a helper class to log traits from a TraitProvider, will remove substantial duplicated code from CPRC and MJBTL

324 lines of code changed in 8 files:

msuchard 2010-05-29 05:44 Rev.: 3196

Fixed feature in jittering continuous traits that only appeared to be fabricating data when really missing

19 lines of code changed in 2 files:

msuchard 2010-05-28 07:23 Rev.: 3194

Fixed bug in ascertainment correction (miscounted) and implemented in BEAGLE. Genomic-wide SNPs here we come!

99 lines of code changed in 7 files:

rambaut 2010-05-28 03:44 Rev.: 3193

Started to implement a branch rate model that takes a realization of a discrete location provided by a MarkovJumpsTreeLikelihood and produces a continuous diffusion rate based on the proportion of time spent in each location and a vector of relative rates and indicators. Builds but not finished implementing.

93 lines of code changed in 2 files:

msuchard 2010-05-28 03:24 Rev.: 3192

Maintaining functional compatibility between ASTL and ASBTL. Need to figure out how to ditch one.

411 lines of code changed in 13 files:

dong.w.xie 2010-05-27 10:27 Rev.: 3189

TRUNK: revert Issue 310 and create ANT to generate beast-beagle-all.jar which includes beast.jar and default main class

21 lines of code changed in 1 file:

dong.w.xie 2010-05-26 11:23 Rev.: 3186

TRUNK: solve Issue 310: beast-beagle.jar not include beast.jar and no default main class

2 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-05-26 04:25 Rev.: 3185

adding "tree" and "alignment" strings to output

4 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-05-26 03:42 Rev.: 3184

the jitter method now updates non-missing values in traits only

9 lines of code changed in 1 file:

philippe.lemey@gmail.com 2010-05-26 02:48 Rev.: 3183

the jitter method now ignores traits with a missing value in any dimension

10 lines of code changed in 1 file:

rambaut 2010-05-25 00:24 Rev.: 3181

Adding backbone to local clock model.

10 lines of code changed in 1 file:

msuchard 2010-05-21 13:19 Rev.: 3178

Can now simulate sequences under a branch-specific substitution model; for example, different dN/dS per branch.

160 lines of code changed in 6 files:

msuchard 2010-05-21 11:42 Rev.: 3177

Parameters can now be randomized at initialization; good for starting from overdispersed states and for simulation studies:

<beast>

<parameter id="test1" dimension="2">
<randomize>
<normalDistributionModel>
<mean> -5 </mean>
<precision> 1.0 </precision> </normalDistributionModel>
</randomize>
</parameter>

<parameter id="test2" value="1 2 3 4"/>

<report>
<parameter idref="test1"/>
</report>

<report>
<parameter idref="test2"/>
</report>

</beast>

32 lines of code changed in 1 file:

msuchard 2010-05-21 10:55 Rev.: 3176

Keeping AncestralState(Beagle)TreeLikelihoods up-to-date

115 lines of code changed in 2 files:

rambaut 2010-05-21 03:13 Rev.: 3175

Accidentally deleted OldTreesPanel.

535 lines of code changed in 1 file:

rambaut 2010-05-21 03:09 Rev.: 3174

Tweak to the hypermutant model

55 lines of code changed in 3 files:

msuchard 2010-05-17 11:00 Rev.: 3170

Preparing MarkovJumps to compute null distributions for tests of selection using just nucleotide models (fast, fast, fast)

435 lines of code changed in 9 files:

msuchard 2010-05-17 05:06 Rev.: 3169

Daniel found a more stable dynamic rescaling -- add a makeDirty()

6 lines of code changed in 1 file:

rambaut 2010-05-11 01:49 Rev.: 3165

Fixed an issue with root optimization for some trees in PathOGen.

847 lines of code changed in 15 files:

alexei.drummond 2010-05-10 15:35 Rev.: 3163

test case for Yule with one "reference" calibration

0 lines of code changed in 1 file:

dong.w.xie 2010-05-07 10:43 Rev.: 3161

TRUNK: merge Issue 307: BEAUti missing .txt in tree log using EBSP

4 lines of code changed in 1 file:

rambaut 2010-05-04 02:16 Rev.: 3156

Added ability to drag and drop files into the file table of LogCombiner and the input file box of TreeAnnotator.

44 lines of code changed in 2 files:

msuchard 2010-05-02 15:25 Rev.: 3154

Better solution for dynamic scaling; still need to find bug (?)

6 lines of code changed in 1 file:

msuchard 2010-05-02 15:09 Rev.: 3153

Temporary solution for dynamic scaling; still need to find bug

13 lines of code changed in 1 file:

msuchard 2010-05-01 10:44 Rev.: 3152

Already fixing bugs in ancestral reconstruction with ASRV

26 lines of code changed in 1 file:

msuchard 2010-05-01 10:07 Rev.: 3151

Updating MarkovJumps and ancestral reconstruction to support across-site-rate-variation models

148 lines of code changed in 6 files:

April 2010 »

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