March 2010 Commit Log

Number of Commits:
89
Number of Active Developers:
8
dong.w.xie 2010-03-31 16:23 Rev.: 3093

TRUNK: BEAUti struggling in discrete traits generator, but not working yet.

366 lines of code changed in 11 files:

dong.w.xie 2010-03-31 13:54 Rev.: 3092

TRUNK: BEAUti fix a bug in Trait table.

5 lines of code changed in 2 files:

dong.w.xie 2010-03-31 13:37 Rev.: 3091

TRUNK: BEAUti make taxonList static.

61 lines of code changed in 13 files:

dong.w.xie 2010-03-31 13:21 Rev.: 3090

TRUNK: BEAUti discrete traits prior and operator panels are working.

267 lines of code changed in 18 files:

dong.w.xie 2010-03-30 17:23 Rev.: 3089

TRUNK: BEAUti discrete traits clock model panel is working.

78 lines of code changed in 3 files:

dong.w.xie 2010-03-29 11:38 Rev.: 3082

TRUNK: enable math junit tests.

2 lines of code changed in 1 file:

dong.w.xie 2010-03-29 10:41 Rev.: 3081

TRUNK: BEAUti discrete traits site model panel is working.

312 lines of code changed in 9 files:

dong.w.xie 2010-03-27 22:31 Rev.: 3080

TRUNK: BEAUti struggling in new discrete traits GUI to fit with BEAUti partitions framework.

550 lines of code changed in 23 files:

msuchard 2010-03-27 11:58 Rev.: 3079

Completed UnitTest for simulation via Uniformization; added UniformizedSubstitutionModel to connect MarkovJumpsTreeLikelihood with the Uniformization method

160 lines of code changed in 5 files:

msuchard 2010-03-27 11:12 Rev.: 3078

Changing output options for CompleteHistorySimulator

28 lines of code changed in 2 files:

msuchard 2010-03-27 10:42 Rev.: 3077

Patched ConvertAlignment so that it will convert a codon alignment into nucleotides.

24 lines of code changed in 1 file:

dong.w.xie 2010-03-26 17:54 Rev.: 3076

TRUNK: BEAUti Phylogeographic fix a bug, but still not complete.

34 lines of code changed in 10 files:

dong.w.xie 2010-03-26 16:15 Rev.: 3075

TRUNK: BEAUti Phylogeographic big update to treat traits as partition data, not complete yet.

514 lines of code changed in 33 files:

msuchard 2010-03-26 11:04 Rev.: 3074

Added methods to simulate end-conditioned CTMC using the Uniformization method; this is the most optimal, simulation algorithm available and should make Stochastic Mapping and Coalescent-with-Migration models much, much faster (when real eigen decompositions are not available ... if the model is real diagonalizable MarkovJumps is still the way to go)

518 lines of code changed in 5 files:

dong.w.xie 2010-03-25 17:09 Rev.: 3073

TRUNK: BEAUti a correction of *BEAST pop size model type.

3 lines of code changed in 2 files:

dong.w.xie 2010-03-25 16:56 Rev.: 3072

TRUNK: BEAUti Phylogeographic generator for general discrete traits.

237 lines of code changed in 13 files:

msuchard 2010-03-25 13:02 Rev.: 3071

Can now simulate (and report) the complete history of any model in BEAST, most importantly codon models (with branch rate variation) and report the true number of synonymous and nonsynonymous mutations in a synthetic dataset.

930 lines of code changed in 12 files:

msuchard 2010-03-25 06:23 Rev.: 3070

Further work for RobustCounting

368 lines of code changed in 9 files:

dong.w.xie 2010-03-24 16:16 Rev.: 3069

TRUNK: BEAUti Phylogeographic improve gui to suit general discrete traits.

480 lines of code changed in 14 files:

msuchard 2010-03-24 12:41 Rev.: 3068

Fixed a couple bugs with the output

29 lines of code changed in 1 file:

dong.w.xie 2010-03-23 16:56 Rev.: 3067

TRUNK: BEAUti Phylogeographic initial dev done for gui.

198 lines of code changed in 12 files:

dong.w.xie 2010-03-22 13:44 Rev.: 3066

TRUNK: BEAUti start generator for location subst model and general subst model.

184 lines of code changed in 9 files:

dong.w.xie 2010-03-22 11:45 Rev.: 3065

TRUNK: BEAUti definitely this time.

2 lines of code changed in 2 files:

dong.w.xie 2010-03-22 11:40 Rev.: 3064

TRUNK: BEAUti fix build this time.

4 lines of code changed in 1 file:

dong.w.xie 2010-03-22 11:38 Rev.: 3063

TRUNK: BEAUti fix build.

4 lines of code changed in 2 files:

dong.w.xie 2010-03-22 11:29 Rev.: 3062

TRUNK: BEAUti more dev for location subst model.

287 lines of code changed in 16 files:

dong.w.xie 2010-03-19 15:10 Rev.: 3061

TRUNK: BEAUti initial dev for location subst model.

163 lines of code changed in 4 files:

dong.w.xie 2010-03-19 13:58 Rev.: 3060

TRUNK: revert unsuccessful correction in r3051, which needs to change name with prefix as well.

3 lines of code changed in 1 file:

dong.w.xie 2010-03-19 13:27 Rev.: 3059

TRUNK: contine to dev new trait in BEAUti.

137 lines of code changed in 6 files:

bloomquist 2010-03-19 08:57 Rev.: 3057

Updated getInverseIntensity() so that when growthRate = 0, it matches up with getIntensity().

4 lines of code changed in 2 files:

msuchard 2010-03-19 08:10 Rev.: 3056

Increasing code re-use

33 lines of code changed in 2 files:

rambaut 2010-03-18 18:32 Rev.: 3055

Added ability to import FASTA format files in BEAUti. Should probably allow extraction of individual fields from label line.

247 lines of code changed in 5 files:

dong.w.xie 2010-03-18 17:33 Rev.: 3054

TRUNK: initial dev for new trait in BEAUti.

366 lines of code changed in 12 files:

bloomquist 2010-03-18 12:58 Rev.: 3053

Finished up getInverseIntensity() for the CataclysmicDemographic model. Checked against getIntensity() so that getInverseIntensity(getIntensity(t)) = t. This occurs.

13 lines of code changed in 1 file:

rambaut 2010-03-18 12:32 Rev.: 3052

Fixed an issue with FlexibleTree not reading trees without translation tables.

2 lines of code changed in 1 file:

dong.w.xie 2010-03-18 09:11 Rev.: 3051

TRUNK: BEAUti: make a unique parameters and operators map.

3 lines of code changed in 1 file:

alexander.alekseyenko 2010-03-18 02:22 Rev.: 3050

Fixed a small bug that prevented beagle from using multiple instances when certain patterns are used.

30 lines of code changed in 1 file:

dong.w.xie 2010-03-17 14:11 Rev.: 3049

TRUNK: update package structure by adding tracer dependency.

125 lines of code changed in 6 files:

dong.w.xie 2010-03-17 13:54 Rev.: 3048

TRUNK: tracer optimize imports.

6 lines of code changed in 3 files:

dong.w.xie 2010-03-16 11:23 Rev.: 3047

TRUNK: merge Issue 287 from branch 1.5.

23 lines of code changed in 3 files:

dong.w.xie 2010-03-16 10:44 Rev.: 3044

TRUNK: merge Issue 288 from branch 1.5.

5 lines of code changed in 3 files:

dong.w.xie 2010-03-16 10:08 Rev.: 3042

TRUNK: merge Issue 286 from branch 1.5.

6 lines of code changed in 1 file:

dong.w.xie 2010-03-15 15:34 Rev.: 3040

TRUNK: time irreversible test (not JUnit).

120 lines of code changed in 1 file:

dong.w.xie 2010-03-12 18:08 Rev.: 3039

TRUNK: time irreversible test, not working yet.

196 lines of code changed in 1 file:

msuchard 2010-03-12 11:40 Rev.: 3038

Trimming code from MarkovJumpCore

49 lines of code changed in 2 files:

alexei.drummond 2010-03-12 11:25 Rev.: 3037

Fixed BirthDeathSerialSampling model. It turns out that death needs to be parameterized relative to birth to get good mixing as they are extremely highly correlated in the data sets I have looked at. I have added the option to parameterize relative or absolute death rate.

36 lines of code changed in 5 files:

dong.w.xie 2010-03-11 15:05 Rev.: 3036

Trunk: solve Issue 285: ComplexSubstitutionModelParser can only refer to SVS not ComplexSubstitutionModel.

1 lines of code changed in 1 file:

alexei.drummond 2010-03-08 16:50 Rev.: 3033

Added elevation-based random walks on GTOPO30 maps

178 lines of code changed in 13 files:

rambaut 2010-03-08 10:30 Rev.: 3032

Updated phylogeography discrete trait example XML. Also, a framework for implementing this in BEAUti.

206 lines of code changed in 5 files:

msuchard 2010-03-08 08:16 Rev.: 3031

Added mean square error estimator to traceAnalysis; could build this feature into Tracer for users doing simulations

64 lines of code changed in 7 files:

msuchard 2010-03-07 19:34 Rev.: 3030

Missed one reference

1 lines of code changed in 1 file:

msuchard 2010-03-07 08:27 Rev.: 3029

Generifying tree trait statistics so they work for both sampled and integrated internal and root nodes; for integrated models, these statistics are now stochastic (i.e. they rely on a full conditional draw of states)

40 lines of code changed in 7 files:

msuchard 2010-03-06 13:08 Rev.: 3028

WishartDistribution.logPdf now takes negligible time in diffusion model (was 20% with sequence data)

55 lines of code changed in 1 file:

rambaut 2010-03-06 11:13 Rev.: 3027

Forgot to commit the changes to BeastMain for the beagle scaling options

7 lines of code changed in 1 file:

rambaut 2010-03-06 11:07 Rev.: 3026

Re-implemented scaling in BeagleTreeLikelihood. This attempts to turn on BEAGLE_AUTO_SCALE and if that fails, uses a dynamic scaling scheme. This recomputes scaling factors every 10,000 evaluations (hard coded at the moment) or if the sum log likelihood is infinite. These options can be controlled on the command line using the -beagle_scaling option ("default", "none", "dynamic" or "always). The "default" option has the behaviour above, the others give the scaling scheme specified.

157 lines of code changed in 3 files:

msuchard 2010-03-06 09:27 Rev.: 3025

Fixed degrees-of-freedom bug in PrecisionGibbsOperator

107 lines of code changed in 6 files:

alexei.drummond 2010-03-05 19:45 Rev.: 3024

Further tweaks on GTOPO30 support

118 lines of code changed in 2 files:

msuchard 2010-03-05 17:28 Rev.: 3023

Moving extensive debugging code out of base class to make code more readable

350 lines of code changed in 4 files:

alexei.drummond 2010-03-05 15:40 Rev.: 3022

Added initial support for reading, tiling and coloring GTOPO30 digital elevation data

237 lines of code changed in 3 files:

msuchard 2010-03-05 13:04 Rev.: 3021

Making progress on Gibbs sampling the fully conjugate diffusion model; taking days longer than I expected

190 lines of code changed in 8 files:

msuchard 2010-03-04 14:52 Rev.: 3020

Added FullyConjugateMultivariateTraitLikelihood; the Gibbs sampler to come next

401 lines of code changed in 8 files:

dong.w.xie 2010-03-04 10:26 Rev.: 3018

Trunk: solve Issue 282: BEAUti: AlignmentGenerator cannot print sequence with long sites properly.

68 lines of code changed in 7 files:

msuchard 2010-03-04 08:51 Rev.: 3017

Refactoring IntegratedMultivariateTraitLikelihood to allow for semi- and fully-conjugate priors on the root node (fully-conjugate allows for Gibbs sampling of the precision matrix)

329 lines of code changed in 3 files:

msuchard 2010-03-03 17:28 Rev.: 3016

Some thoughts on Gibbs sampling the precision matrix

118 lines of code changed in 2 files:

dong.w.xie 2010-03-03 16:01 Rev.: 3015

Trunk refactoring: fix a bug of duplcation parser name in GMRF Skyride Likelihood.

8 lines of code changed in 3 files:

msuchard 2010-03-03 12:49 Rev.: 3014

Delegating funcationality in IntegratedMultivariateTraitLikelihood for profiling and future refactoring into a TraitLikelihoodCore

279 lines of code changed in 7 files:

dong.w.xie 2010-03-03 10:42 Rev.: 3013

Trunk refactoring: finish MULTIVARIATE OU PROCESS (split parsers).

689 lines of code changed in 28 files:

dong.w.xie 2010-03-03 08:46 Rev.: 3012

Trunk refactoring: finish MSSD (split parsers).

441 lines of code changed in 16 files:

msuchard 2010-03-03 07:53 Rev.: 3011

What is a marginal likelihood?

1 lines of code changed in 1 file:

rambaut 2010-03-03 05:12 Rev.: 3010

AMTL now can take a leaf trait parameter directly. Actually this would be best removed all together (if a leaf trait param from a tree model is supplied then it is used otherwise it just copies the traits out of the taxa when they are used to populate the caches).

75 lines of code changed in 2 files:

msuchard 2010-03-03 04:03 Rev.: 3009

Adding different output formats for RobustCounting

113 lines of code changed in 3 files:

philippe.lemey@gmail.com 2010-03-03 02:34 Rev.: 3008

Timeslicer bug fixing

13 lines of code changed in 1 file:

rambaut 2010-03-03 01:16 Rev.: 3007

Stored cached arrays were not being allocated. Turning cacheBranches="true" now runs (whether it works is yet to be determined).

7 lines of code changed in 1 file:

dong.w.xie 2010-03-02 16:44 Rev.: 3006

Trunk refactoring: finish indel (split parsers).

183 lines of code changed in 12 files:

dong.w.xie 2010-03-02 15:08 Rev.: 3005

Trunk refactoring: organize Data Tpye parser (split parsers).

109 lines of code changed in 3 files:

dong.w.xie 2010-03-02 14:07 Rev.: 3004

Trunk refactoring: finish GMRF (split parsers).

569 lines of code changed in 19 files:

dong.w.xie 2010-03-02 13:21 Rev.: 3003

Trunk refactoring: finish trace (split parsers).

555 lines of code changed in 15 files:

dong.w.xie 2010-03-02 10:24 Rev.: 3002

Trunk refactoring: finish Logger (split parsers).

1034 lines of code changed in 19 files:

dong.w.xie 2010-03-02 10:05 Rev.: 3001

Trunk refactoring: finish MCMC (split parsers).

255 lines of code changed in 6 files:

dong.w.xie 2010-03-02 09:47 Rev.: 3000

Trunk refactoring: 3rd part of operators (split parsers).

611 lines of code changed in 35 files:

msuchard 2010-03-02 04:56 Rev.: 2999

Default should have no debug info printed

1 lines of code changed in 1 file:

rambaut 2010-03-02 01:23 Rev.: 2998

Updated beagle.jar

0 lines of code changed in 1 file:

rambaut 2010-03-02 01:23 Rev.: 2997

The line pointing to SimpleOperatorSchedule in release_parsers.properties was pointing to dr.inferencexml.operators.SimpleOperatorSchedule even though this parser hasn't been moved yet. This causes all MCMC elements to fail to parse.



1 lines of code changed in 1 file:

rambaut 2010-03-02 01:17 Rev.: 2996

SetOperatorParser is wrongly named ('SetOperatorparser') - as this is a difference only in the case, I am changing it to another name and then back to the correct name. I have found that just changing the case can cause problems in some OSs.

60 lines of code changed in 2 files:

rambaut 2010-03-02 01:11 Rev.: 2995

SetOperatorParser is wrongly named ('SetOperatorparser') - as this is a difference only in the case, I am changing it to another name and then back to the correct name. I have found that just changing the case can cause problems in some OSs.

0 lines of code changed in 2 files:

Sibon.Li@gmail.com 2010-03-01 15:31 Rev.: 2994

Fixed the parameterisation of the burnin to that of the LogAnalyser (instead of the TreeAnnotator)

1 lines of code changed in 1 file:

dong.w.xie 2010-03-01 13:11 Rev.: 2993

Trunk refactoring: 2nd part of operators (split parsers).

789 lines of code changed in 37 files:

msuchard 2010-03-01 12:24 Rev.: 2992

Updating robust counting output

13 lines of code changed in 2 files:

msuchard 2010-03-01 09:27 Rev.: 2991

Robust counting is working (as far as I can tell) and returns expected numbers of syn and non-syn changes on a tree, using just nucleotide models

318 lines of code changed in 8 files:

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