November 2010 Commit Log

Number of Commits:
46
Number of Active Developers:
7
dong.w.xie 2010-11-30 16:03 Rev.: 3733

Trunk: fix JUnit

3 lines of code changed in 1 file:

dong.w.xie 2010-11-30 13:42 Rev.: 3732

Trunk: solve Issue 435: UniformIntegerOperator did not include upper in the value:

int newValue = MathUtils.nextInt(upper - lower) + lower;
Because nextInt(n) gives value [0, n-1], if upper = 2 then newValue cannot have 2.
The correct code should be
int newValue = MathUtils.nextInt(upper - lower + 1) + lower;

47 lines of code changed in 3 files:

dong.w.xie 2010-11-30 09:13 Rev.: 3731

Trunk: make Integer Parameter to allow to pass Variable<Integer>.

534 lines of code changed in 14 files:

rambaut 2010-11-26 23:45 Rev.: 3730

Added a test and an error to avoid a type casting error when -beagle_instances is used in conjunction with codon partitioning.

3 lines of code changed in 1 file:

jheled 2010-11-21 17:51 Rev.: 3729

Add chs, log and exp tp RPN calculator
Add Tree height statistic parser tp .properties

Special calibration cases use RPN expression.

170 lines of code changed in 7 files:

philippe.lemey@gmail.com 2010-11-20 01:26 Rev.: 3728

Adding -/N/+ classification to DnDsPerSiteAnalysis

52 lines of code changed in 1 file:

rambaut 2010-11-18 09:49 Rev.: 3727

Improvements to the Guess Dates Dialog to allow for parsing of calendar dates.

301 lines of code changed in 2 files:

rambaut 2010-11-17 09:47 Rev.: 3726

A bit of a hack but if the RegEx function of DateGuesser doesn't like the number it tries to parse it as a calendar date.

27 lines of code changed in 2 files:

rambaut 2010-11-16 22:14 Rev.: 3725

Added an alternative Continous Tree KML generator (TreeKMLGenerator).

1655 lines of code changed in 12 files:

dong.w.xie 2010-11-16 14:19 Rev.: 3724

Trunk: update New Tracer doc, because key word "category" is changed into "categorical".

2 lines of code changed in 4 files:

rambaut 2010-11-16 11:11 Rev.: 3723

Added ability to specify a list of HPD densities to add contours for.

71 lines of code changed in 1 file:

rambaut 2010-11-16 10:17 Rev.: 3722

Removed -d32 switch from the Mac version's command line script

1 lines of code changed in 2 files:

rambaut 2010-11-16 05:18 Rev.: 3721

Cleaned up full evaluation test error reporting.

5 lines of code changed in 1 file:

rambaut 2010-11-16 05:14 Rev.: 3720

Started work on caching in ATL

95 lines of code changed in 2 files:

rambaut 2010-11-15 22:40 Rev.: 3719

Adding metadata into KML output layers in TimeSlicer

109 lines of code changed in 7 files:

philippe.lemey@gmail.com 2010-11-15 21:48 Rev.: 3718

TimeSlicer update for compatibility with Google Earth 5.2 / cartographica

1 lines of code changed in 1 file:

rambaut 2010-11-15 21:45 Rev.: 3717

TreeTraitParserUtilities now picks up trait parameters that are either simply called the taxon name or have the trait name appended.

8 lines of code changed in 1 file:

rambaut 2010-11-14 23:40 Rev.: 3716

Started to add 'ExtendedData' into the KML output of TimeSlicer. This will be better for use in GIS software, allowing styling by data such as time.

112 lines of code changed in 1 file:

msuchard 2010-11-13 09:45 Rev.: 3715

Tweaks to AntigenicTraitLikelihood (consider renaming to MultidimensionalScalingLikelihood) as that class returns finite likelihood. Added default bounds to dimension-changing MatrixParameter.

5 lines of code changed in 2 files:

rambaut 2010-11-13 08:33 Rev.: 3714

AntigenicTraitLikelihood runs! Unlikely to work though. Changed MatrixParameter to set dimensions lazily. TreeTraitParserUtility now labels the individual rows of the compound parameter just as taxon labels so that ATL can pick them up.

268 lines of code changed in 5 files:

jheled 2010-11-12 15:59 Rev.: 3713

First implementation of correct calibration density for one monophyletic clade inside a Yule tree.

Allow an "explicit" correction via pre computed coefficients, used when putting additional constraints on the topology

43 lines of code changed in 5 files:

rambaut 2010-11-12 05:17 Rev.: 3712

Added AntigenicTraitLikelihood to parser list.

1 lines of code changed in 1 file:

rambaut 2010-11-12 03:16 Rev.: 3711

Add release files for Phylogeography tools

143 lines of code changed in 7 files:

rambaut 2010-11-12 03:14 Rev.: 3710

Added package building to the phylogeography ant file.

31 lines of code changed in 1 file:

rambaut 2010-11-12 02:58 Rev.: 3709

Added argument parsing to ContinuousTreeToKML

117 lines of code changed in 3 files:

msuchard 2010-11-12 02:11 Rev.: 3708

Temporary patch for bug in ARG model in which negative branch lengths arise.

18 lines of code changed in 2 files:

rambaut 2010-11-12 01:46 Rev.: 3707

Created an ANT file for phylogeography stuff.

543 lines of code changed in 5 files:

rambaut 2010-11-12 00:52 Rev.: 3706

Consolidated phylogeography command-line tools in one place.

2127 lines of code changed in 11 files:

rambaut 2010-11-11 23:49 Rev.: 3705

Moved command line KML generating phylogenetic tools over from FigTree repository.

3346 lines of code changed in 4 files:

jheled 2010-11-11 22:26 Rev.: 3704

First implementation of correct calibration density for one monophyletic clade inside a Yule tree.

The internal interface it a little clunky since the concept does not fit well with the current classes implementing the various speciation priors.

The XML interface is via an additional 'calibration' element inside
the speciationLikelihood. The element contains the taxa and a distribution for the root of the taxa. For a single taxon list, the distribution is for the parent of the taxon, which has no other constraints.

<speciationLikelihood id="speciationlike">
<model>
<yuleModel idref="yule"/>
</model>
<speciesTree>
<treeModel idref="treeModel"/>
</speciesTree>

<calibration>
<exponentialDistributionModel>
<mean>
<parameter id="mean" value="1"/>
</mean>
</exponentialDistributionModel>
<taxa>
<taxon idref="tip1"/>
<taxon idref="tip2"/>
</taxa>
</calibration>
</speciationLikelihood>

158 lines of code changed in 10 files:

jheled 2010-11-11 22:16 Rev.: 3703

automatic intelliJ minor syntax fixes

8 lines of code changed in 6 files:

akaruiws 2010-11-10 18:01 Rev.: 3702

add new constructor.

18 lines of code changed in 2 files:

jheled 2010-11-09 11:52 Rev.: 3701

Allows any number of tempratures in command line

92 lines of code changed in 2 files:

rambaut 2010-11-05 21:56 Rev.: 3700

Added utility class for reading and handling tabular data and applied it to loading an HI table.

156 lines of code changed in 2 files:

rambaut 2010-11-05 05:16 Rev.: 3699

Set default posterior limit in TreeAnnotator dialog box to zero to match commandline behaviour.

1 lines of code changed in 2 files:

msuchard 2010-11-05 04:14 Rev.: 3698

More work on AntigenicTraitLikelihood; should now implement the Oh and Raftery sampling density. Priors are still needed.

73 lines of code changed in 1 file:

dong.w.xie 2010-11-04 15:26 Rev.: 3697

Trunk: Exception for easy debug.

1 lines of code changed in 1 file:

rambaut 2010-11-04 11:04

More work on AntigenicTraitLikelihood

136 lines of code changed in 2 files:

rambaut 2010-11-04 09:39 Rev.: 3694

Updated trunk's Laplace Prior Parser to use 'scale' rather than 'stdev' (to match the output of BEAUti and the parser in the 1.6 branch).

3 lines of code changed in 1 file:

rambaut 2010-11-04 03:57 Rev.: 3693

Fixed an error loading non-binary trees (i.e., most unrooted trees).

2 lines of code changed in 1 file:

rambaut 2010-11-04 01:01 Rev.: 3692

Final tweaks to new version of Pathogen

43 lines of code changed in 3 files:

rambaut 2010-11-03 22:28 Rev.: 3691

84 lines of code changed in 1 file:

rambaut 2010-11-03 20:09 Rev.: 3690

Pathogen loads Newick tree files now.

35 lines of code changed in 1 file:

rambaut 2010-11-03 05:10 Rev.: 3689

Started work on a class for handling antigenic assay data.

70 lines of code changed in 1 file:

rambaut 2010-11-02 21:25 Rev.: 3688

Added a 'delta' parameter to the AbstractMultivariateTraitLikelihood. This adds a bit of error to the tip data. This could have been done using a BranchRateModel but I wanted it to be added after rescaling by tree length. The disadvantage of this approach is we can't sample the locations of the tips.

67 lines of code changed in 3 files:

alexei.drummond 2010-11-02 10:10 Rev.: 3687

Added model-specitic parameter-maskable model averaging across trees to speciation model framework

347 lines of code changed in 4 files:

October 2010 »

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