October 2012 Commit Log

Number of Commits:
30
Number of Active Developers:
10
msuchard 2012-10-28 14:36 Rev.: 5211

Implemented transposed matrix representations for multilocus branch rate models

113 lines of code changed in 5 files:

mdhall272@gmail.com 2012-10-27 03:45 Rev.: 5210

Should now co-estimate epidemiological parameters on a fixed tree

53 lines of code changed in 3 files:

alexander.alekseyenko 2012-10-26 09:32 Rev.: 5209

Updated Compound DirichletMultinomial distribution to use both the rates and frequencies + dispersion parametrization. New example XML included.

176 lines of code changed in 3 files:

fbielejec 2012-10-26 00:15 Rev.: 5208

user can cancel his choice and return to defaults

276 lines of code changed in 14 files:

Sibon.Li@gmail.com 2012-10-25 15:23 Rev.: 5207

RandomDiscretizedBranchRates has been renamed to the more meaningful ContinuousBranchRates. RandomDiscretizedBranchRatesParser has been kept and throws an error in the unlikely case that someone actually has been using this implementation.

390 lines of code changed in 8 files:

mtolkoff@gmail.com 2012-10-25 09:49 Rev.: 5206

reverts to previous version

50 lines of code changed in 1 file:

mtolkoff@gmail.com 2012-10-25 08:02 Rev.: 5205

Adds commented out broken code

114 lines of code changed in 2 files:

mdhall272@gmail.com 2012-10-24 05:03 Rev.: 5204

fixed trivial error

0 lines of code changed in 1 file:

fbielejec 2012-10-23 02:42 Rev.: 5203

compile the partitions before simulating

85 lines of code changed in 5 files:

fbielejec 2012-10-23 00:21 Rev.: 5202

pop out dialogs with settings

772 lines of code changed in 14 files:

fbielejec 2012-10-20 06:04 Rev.: 5201

added action button

35 lines of code changed in 2 files:

fbielejec 2012-10-20 01:27

adding partitions to the UI

928 lines of code changed in 14 files:

mtolkoff@gmail.com 2012-10-19 09:15 Rev.: 5198

Test commit; no functionality changes

11 lines of code changed in 1 file:

fbielejec 2012-10-19 05:02 Rev.: 5197

adding partitions to the UI

497 lines of code changed in 11 files:

rambaut 2012-10-14 07:17 Rev.: 5196

BEAUti now generates a hierarchical coalescent simulator that generates monophyletic groups and required clade heights. Clade heights can be given in the Taxon Sets table in the column called 'age'. These should lie inside any hard prior bounds (this is not done automatically).

104 lines of code changed in 12 files:

mdhall272@gmail.com 2012-10-12 05:33 Rev.: 5195

Ooops. Reverted.

18 lines of code changed in 1 file:

mdhall272@gmail.com 2012-10-12 05:31 Rev.: 5194

Committed work to date on network reconstruction method

1521 lines of code changed in 10 files:

rambaut 2012-10-11 02:35 Rev.: 5193

Created a new cleaner coalescent simulator parser to help generate nested subtrees from taxon sets. Updating BEAUti to generate simulated trees that conform to monophyly constrants and hard bounds on tmrcas.

188 lines of code changed in 5 files:

graham853@gmail.com 2012-10-10 00:19 Rev.: 5192

Allopolyploid model. Added MCMC operator to flip legs and sequences of tetraploid tree to improve mixing. Improved sampling for initial state of network. Added statistic for number of hybridizations.

1287 lines of code changed in 12 files:

alexei.drummond 2012-10-09 15:51 Rev.: 5191

Added a hack to get rough time-tree out of Pathogen

59 lines of code changed in 3 files:

fbielejec 2012-10-09 02:46

working on the UI

32 lines of code changed in 5 files:

msuchard 2012-10-07 05:18 Rev.: 5187

Improved parsing for CPRC.

10 lines of code changed in 1 file:

fbielejec 2012-10-07 02:44 Rev.: 5186

added padding with gaps for taxa unique for partitions

25 lines of code changed in 1 file:

msuchard 2012-10-05 09:02 Rev.: 5185

Started a wrapper to provide the transpose of a MatrixParameter

74 lines of code changed in 1 file:

mdhall272@gmail.com 2012-10-03 00:44 Rev.: 5184

Allowed to take infinite maximum or minimum values

21 lines of code changed in 2 files:

baele.guy@gmail.com 2012-10-02 08:34 Rev.: 5183

Log transformed kernel density estimation can also be used in Tracer

2 lines of code changed in 2 files:

baele.guy@gmail.com 2012-10-02 08:33 Rev.: 5182

Added log transformed kernel density estimation to the list

1 lines of code changed in 2 files:

baele.guy@gmail.com 2012-10-02 08:31 Rev.: 5181

Kernel density estimation for densities with bounded support by using log transformation

382 lines of code changed in 1 file:

baele.guy@gmail.com 2012-10-02 08:28 Rev.: 5180

Additional output column for stepping-stone column

12 lines of code changed in 2 files:

baele.guy@gmail.com 2012-10-02 08:28 Rev.: 5179

Additional output column for path sampling

12 lines of code changed in 2 files:

September 2012 »

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