August 2008 Commit Log

Number of Commits:
81
Number of Active Developers:
7
rambaut 2008-08-30 20:49 Rev.: 1172

Some additions to the sequence simulator

133 lines of code changed in 3 files:

rambaut 2008-08-30 07:27 Rev.: 1171

Updated jebl library

5 lines of code changed in 2 files:

rambaut 2008-08-29 06:06 Rev.: 1170

Started work on a sequence simulator

275 lines of code changed in 5 files:

alexander.alekseyenko 2008-08-23 05:03 Rev.: 1169

1) added Ferreira-Suchard prior on branch length/ctmc scale parameter
2) cleaned out priors for MSSD, xml example updated
3) Added an option to NewickParser to scale the tree to a specified total length

139 lines of code changed in 7 files:

alexei.drummond 2008-08-23 02:27 Rev.: 1168

refactoring of ALS stuff with Alex

363 lines of code changed in 7 files:

alexander.alekseyenko 2008-08-23 00:32 Rev.: 1167

Gamma prior on death rate for MSSD model and some consistency changes.

232 lines of code changed in 6 files:

alexander.alekseyenko 2008-08-22 22:32 Rev.: 1166

removing redundant files...

0 lines of code changed in 6 files:

alexei.drummond 2008-08-22 20:52 Rev.: 1165

small bug fix in ascertained site patterns parser + RLTV improvements

117 lines of code changed in 6 files:

alexei.drummond 2008-08-21 08:45 Rev.: 1164

tidied up random local clock model. The tree likelihood still dominates time with large alignments, but at least it will run very fast when the alignment is small, or when its run on a simplified likelihood (a la Thorne et al)

111 lines of code changed in 3 files:

alexei.drummond 2008-08-21 07:09 Rev.: 1163

tidying operators

38 lines of code changed in 11 files:

bloomquist 2008-08-21 05:57 Rev.: 1162

Moved my coalescent loggers to evomodel.coalescent package.

836 lines of code changed in 9 files:

alexei.drummond 2008-08-21 02:55 Rev.: 1161

doubled the speed of RandomLocalYuleModel :-)

111 lines of code changed in 2 files:

alexei.drummond 2008-08-21 01:05 Rev.: 1160

more tweaks to random local yule model

24 lines of code changed in 3 files:

alexei.drummond 2008-08-20 23:31 Rev.: 1159

refactored random local stuff so that it can be used for both clock rate and speciation models

608 lines of code changed in 10 files:

alexei.drummond 2008-08-20 09:32 Rev.: 1158

added analysis of special logger

201 lines of code changed in 3 files:

alexei.drummond 2008-08-20 05:20 Rev.: 1157

added special logger for random local yule model

344 lines of code changed in 5 files:

alexei.drummond 2008-08-19 22:53 Rev.: 1156

Added RandomLocalYuleModel and a new move for stochastical variable selection models on trees

1086 lines of code changed in 12 files:

bloomquist 2008-08-19 10:11 Rev.: 1155

Added a SubStatistic class that allows you to select specific dimensions of a specified statistic.

92 lines of code changed in 2 files:

msuchard 2008-08-18 06:41 Rev.: 1154

GMRF Skyride Beauti now defaults to a 1 / log cooling schedule.

55 lines of code changed in 3 files:

alexei.drummond 2008-08-17 23:55 Rev.: 1153

added ability to specify the number of decimal places for branch lengths in the newick format and tree logger. also some tidying

344 lines of code changed in 5 files:

msuchard 2008-08-17 15:02 Rev.: 1152

Added GMRF Skyride as a tree prior option to Beauti.

3618 lines of code changed in 10 files:

rambaut 2008-08-17 08:39 Rev.: 1151

More work on Trees panel

494 lines of code changed in 7 files:

alexei.drummond 2008-08-17 08:03 Rev.: 1150

moved Sebastian's TreeLogger out of inference/loggers. The inference package should not contain any dependencies on evolution or evomodel.

330 lines of code changed in 4 files:

bloomquist 2008-08-17 07:30 Rev.: 1149

A few more small error changes to both classes.

102 lines of code changed in 2 files:

bloomquist 2008-08-17 06:33 Rev.: 1148

Renormalized the GMRF weights by the tree heights. Hopefully resolved conflict in GMRFSkyrideFixedGridLogger with repository.

68 lines of code changed in 2 files:

rambaut 2008-08-17 00:56 Rev.: 1147

More work on Trees panel

294 lines of code changed in 2 files:

rambaut 2008-08-16 23:52 Rev.: 1146

Removed some redundant and out of date code in dr.app.tools (NexusConverter etc).

183 lines of code changed in 7 files:

bloomquist 2008-08-16 16:13 Rev.: 1145

Was calculating the offdiagonal weights at -2 for the uniform smoothing. Changed it to -1. Should have no effect, but -1 is the correct #.

1 lines of code changed in 1 file:

bloomquist 2008-08-16 11:50 Rev.: 1144

Fixed spelling error.

1 lines of code changed in 1 file:

bloomquist 2008-08-16 11:23 Rev.: 1143

Added a uniform smoothing option to the GMRFSkyrideLikelihood.

58 lines of code changed in 3 files:

rambaut 2008-08-16 10:58 Rev.: 1142

Progressing on TreesPanel. More work to be done.

80 lines of code changed in 7 files:

bloomquist 2008-08-16 09:22 Rev.: 1141

Created two Statistic that spit out the coalescent interval lengths and the lineage counts. Also created a fixed grid logger that handles both the mcp skyline and gmrf skyride.

690 lines of code changed in 6 files:

msuchard 2008-08-16 08:23 Rev.: 1140

Fixed ARGAddRemoveOperatorTest so that it actually passes :-)!

19 lines of code changed in 2 files:

alexei.drummond 2008-08-16 02:58 Rev.: 1139

tweaks

31 lines of code changed in 2 files:

Sebastian.Hoehna 2008-08-15 18:44 Rev.: 1138

Some new operators, but still under development. A little tigying up in the old stuff and some minor corrections.

1630 lines of code changed in 10 files:

Sebastian.Hoehna 2008-08-15 18:42 Rev.: 1137

New test cases for the NNI, FNPR and ImportanceSubtreeSwap operators.

402 lines of code changed in 3 files:

Sebastian.Hoehna 2008-08-15 12:44 Rev.: 1136

This test case shows the bug in the Wide Exchange!

64 lines of code changed in 1 file:

msuchard 2008-08-15 12:42 Rev.: 1135

Added a flat prior over ARG space.

283 lines of code changed in 5 files:

Sebastian.Hoehna 2008-08-15 11:50 Rev.: 1134

Some convergence listener, logger and a tree logger which doesn't use the output file.

1209 lines of code changed in 3 files:

rambaut 2008-08-15 11:08 Rev.: 1133

Started work on a TreesPanel. Moved tree prior stuff here. Allow selection of user tree (from those loaded). Other features to be added soon is the ability to do a root to tip plot to check temporal signal. Other tweaks and fixes.

1840 lines of code changed in 18 files:

msuchard 2008-08-15 04:05 Rev.: 1131

Removed YuleModelParser from BeastParser and fixed some XML parsing in MultivariateTraitLikelihood.

6 lines of code changed in 2 files:

alexei.drummond 2008-08-15 03:44 Rev.: 1130

added new tests for wide exchange operator in ExchangeOperatorTest and YuleModelTest... I would encourage other BEAST developers to consider writing JUnit tests... they are easy and fun!

198 lines of code changed in 5 files:

Sebastian.Hoehna 2008-08-14 14:35 Rev.: 1129

I deleted the Listeners since I there weren't working anymore. I think no one was using them. But I got some new ones instead.

0 lines of code changed in 2 files:

Sebastian.Hoehna 2008-08-14 14:27 Rev.: 1128

Added some stuff for estimating the tree probability according to the conditional clade probabilities.

627 lines of code changed in 2 files:

Sebastian.Hoehna 2008-08-14 14:25 Rev.: 1127

Bugfix in the compareTo method for two Clades.

10 lines of code changed in 1 file:

msuchard 2008-08-14 11:09 Rev.: 1126

Port of ARG classes into the trunk. There are some very silly repeats of code (namely: TreeModel and ARGModel should inherit from a base class, ARGTreeLogger is almost indentical to TreeLogger, and CompoundParameter should replace ARGCompoundParameter).

15969 lines of code changed in 33 files:

alexei.drummond 2008-08-14 09:28 Rev.: 1125

added ExchangeOperatorTest

197 lines of code changed in 3 files:

bloomquist 2008-08-13 07:27 Rev.: 1118

Added a feature to print out the random sample in RandomTaxaSample.java in xml format. Also added a logChoose function to the Binomial class for overflow reasons.

64 lines of code changed in 2 files:

msuchard 2008-08-13 07:04 Rev.: 1117

Ported MPI parallelization from branches/arg to trunk. Please check the license on MPJ. If it's OK to distribute then cool ... else I will write a dummy library.

1562 lines of code changed in 12 files:

msuchard 2008-08-13 04:22 Rev.: 1115

Fixed imports in MultivariateDistributionLikelihood after distributions moved to dr.math.distributions ... was not compiling

8 lines of code changed in 1 file:

rambaut 2008-08-12 23:00 Rev.: 1114

Updated jebl library

0 lines of code changed in 1 file:

rambaut 2008-08-12 22:55 Rev.: 1113

Fixed an unwanted import in TracerApp

14 lines of code changed in 2 files:

alexei.drummond 2008-08-12 21:16 Rev.: 1112

moved all distributions into their own sub-package in dr.math

4911 lines of code changed in 76 files:

alexei.drummond 2008-08-12 20:52 Rev.: 1111

Who will delete the most lines without removing functionality? That is the BEAST refactoring challenge for 2008 - simplified PriorDialog further...

2 lines of code changed in 1 file:

alexei.drummond 2008-08-12 20:47 Rev.: 1110

added Laplace distribution in prior options and heavily refactored PriorDialog -- its *much* nicer now, if I do say so myself :-)

584 lines of code changed in 8 files:

alexei.drummond 2008-08-12 09:01 Rev.: 1109

refactoring model panel in BEAUti

818 lines of code changed in 6 files:

rambaut 2008-08-09 20:40 Rev.: 1103

Updated tracers' ant file

1 lines of code changed in 1 file:

rambaut 2008-08-09 20:39 Rev.: 1102

Updated jebl.jar in /lib

0 lines of code changed in 1 file:

jen.tom 2008-08-09 10:44 Rev.: 1101

Added log comment in SimpleOperatorSchedule.

4 lines of code changed in 1 file:

bloomquist 2008-08-09 10:41 Rev.: 1100

Made small error change.

2 lines of code changed in 1 file:

rambaut 2008-08-09 02:41 Rev.: 1099

Renamed ADNADamageModel to SequenceErrorModel. Intend to make it more general.

213 lines of code changed in 4 files:

rambaut 2008-08-08 12:12 Rev.: 1098

More additions and improvements to Tracer

373 lines of code changed in 11 files:

rambaut 2008-08-08 04:14 Rev.: 1097

Some fixes to Tracer: checked reading scientific format. Cleaned up the formating of numbers in the tables and in the plots. Added a yellow colour for 100<ESS<200. Fixed an issue about NaN in trace files - possibly not required.

377 lines of code changed in 10 files:

rambaut 2008-08-07 23:45 Rev.: 1096

Updated version to 1.5beta and build number to match this revision

2 lines of code changed in 1 file:

rambaut 2008-08-07 23:42 Rev.: 1095

Merged some simultaneous changes

2 lines of code changed in 1 file:

alexei.drummond 2008-08-07 23:18 Rev.: 1094

added ability to read in char sets from a nexus file that only take every k'th site

25 lines of code changed in 1 file:

alexei.drummond 2008-08-07 12:40 Rev.: 1093

now treeannotator is really fixed... but it needs a serious refactoring

46 lines of code changed in 1 file:

alexei.drummond 2008-08-07 12:04 Rev.: 1092

Mysterious increment of clade count caused posterior probabilities greater than 1!

858 lines of code changed in 1 file:

alexei.drummond 2008-08-07 08:33 Rev.: 1091

refactoring Prior Panel code in beauti and fixing tmrca(taxonSet) in PriorTable

1145 lines of code changed in 15 files:

alexei.drummond 2008-08-07 08:09 Rev.: 1090

refactored DiscretizedBranchRates parser

178 lines of code changed in 6 files:

alexei.drummond 2008-08-07 05:32 Rev.: 1089

TableSorter didn't have access to these images

0 lines of code changed in 2 files:

alexei.drummond 2008-08-06 14:24 Rev.: 1088

fixes to nexus charset reader

15 lines of code changed in 4 files:

alexei.drummond 2008-08-06 13:38 Rev.: 1087

fixed build_release

9 lines of code changed in 3 files:

alexei.drummond 2008-08-06 08:48 Rev.: 1086

139 lines of code changed in 2 files:

alexei.drummond 2008-08-06 06:39 Rev.: 1085

testCataclysm and some unit test examples of how to test BEAST MCMC without any XML!

581 lines of code changed in 8 files:

rambaut 2008-08-06 03:06 Rev.: 1084

Added an attribute (reflect="upper", reflect="lower" or reflect="both") to RandomWalkOperator to allow reflection at boundaries.

53 lines of code changed in 1 file:

rambaut 2008-08-06 02:48 Rev.: 1083

Got the DNA damage model working.

224 lines of code changed in 11 files:

msuchard 2008-08-05 11:24 Rev.: 1082

Fixed (I think) a potentially nasty bug in the continous model Gibbs operators. PrecisionMatrixGibbsOperator was taking the Wishart prior scale matrix as a rate ( 1 / theta ) matrix. Ooops. Also added a "non-informative" option with the Wishart prior that the operator understands.

187 lines of code changed in 4 files:

rambaut 2008-08-05 01:16 Rev.: 1080

Moved the TreeModelParser into dr.evomodelxml as it was already a separate class. Some refactoring invoved.

1479 lines of code changed in 7 files:

rambaut 2008-08-04 22:42 Rev.: 1079

Added ability to exclude taxa from the speciation model. This results in the speciation prior being calculated on the subtree of the included taxa only.

133 lines of code changed in 3 files:

rambaut 2008-08-04 21:26 Rev.: 1078

Fixes to ExponentialLogistic

12 lines of code changed in 5 files:

July 2008 »

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