Directory src/dr/evolution/tree/

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msuchard 2013-05-08 04:03 Rev.: 5637

Updated MultivariateTraitTree to work with EmpiricalTreeDistribution

0 lines of code changed in 2 files:

• src/dr/evolution/tree: MultivariateTraitTree.java (-3)

msuchard 2013-05-07 07:43 Rev.: 5635

Fixing transformed trees when random

7 lines of code changed in 1 file:

• src/dr/evolution/tree: MultivariateTraitTree.java (+7 -1)

msuchard 2013-05-06 15:27 Rev.: 5631

Finally interfacing multivariate traits, although they are now generally integrated out.

35 lines of code changed in 1 file:

• src/dr/evolution/tree: MultivariateTraitTree.java (+35)

rambaut 2013-02-02 05:17 Rev.: 5376

Porting changes from 1.7

17 lines of code changed in 2 files:

• src/dr/evolution/tree: TreeTraitProvider.java (new)

jheled@gmail.com 2012-12-23 12:48 Rev.: 5299

Add '-heights ca' option to set heights which do not suffer from the "negative branches" problem. citation later ....

26 lines of code changed in 2 files:

• src/dr/evolution/tree: Tree.java (+26)

msuchard 2012-12-20 10:00 Rev.: 5286

Standardizing format for complete histories with single events

7 lines of code changed in 2 files:

• src/dr/evolution/tree: TreeTrait.java (new)

rambaut 2012-12-04 19:37 Rev.: 5274

A better solution to the multithreading issue with trees that avoids thread syncs. The problem was only for empirical trees for which the branch lengths were known but not the node heights. Thus it had to compute the node heights when asked and this caused the thread conflict. Now the EmpiricalTrees object forces a node height calculation prior to evaluation.

8 lines of code changed in 2 files:

• src/dr/evolution/tree: FlexibleTree.java (+8 -8)

graham853@gmail.com 2012-09-15 02:40 Rev.: 5162

Allopolyploid model: new version of ChangeNumHybridizations move and bug fixes.

5 lines of code changed in 2 files:

• src/dr/evolution/tree: SlidableTree.java (+5 -6)

rambaut 2012-08-04 03:49 Rev.: 5097

Porting fixes from 1.7.3 back into the trunk

8 lines of code changed in 1 file:

• src/dr/evolution/tree: Tree.java (+8 -1)

graham853@gmail.com 2012-07-17 02:28 Rev.: 5071

Code for n diploids, one hybridization now working. Experimental code (PopsIO) added for multispecies coalescent with population size parameters integrated out.

131 lines of code changed in 1 file:

• src/dr/evolution/tree: SlidableTree.java (+131 -111)

rambaut 2012-06-27 09:32 Rev.: 5050

Fixed issue with trees with polytomies having bad branch lengths.

1 lines of code changed in 1 file:

• src/dr/evolution/tree: FlexibleTree.java (+1)

rambaut 2012-06-27 09:21 Rev.: 5049

Fixed issue with trees with polytomies having bad branch lengths.

8 lines of code changed in 1 file:

• src/dr/evolution/tree: FlexibleTree.java (+8)

msuchard 2012-05-18 00:39 Rev.: 4984

On second thought, it might just be easier to group several TreeParameterModels together. Committing just to keep a record.

36 lines of code changed in 1 file:

• src/dr/evolution/tree: TreeDoubleTraitProvider.java (new 36)

msuchard 2012-05-16 20:46 Rev.: 4971

Added a trait logger for complete histories with times under robust dnds counting

58 lines of code changed in 1 file:

• src/dr/evolution/tree: TreeTrait.java (+58 -2)

graham853@gmail.com 2012-05-10 00:51 Rev.: 4946

Extending allopolyploid model to deal with arbitrary numbers of diploids. Most new code is in new class AlloppDiploidHistory and old class AlloppNetworkNodeSlide.

135 lines of code changed in 1 file:

• src/dr/evolution/tree: SlidableTree.java (+135)

rambaut 2011-11-16 00:45 Rev.: 4429

Made BranchRateModel a TreeTraitProvider so it can be logged more easily. Also added feature to TreeLoggerParser where a tree trait can be specified (with a special tag).

8 lines of code changed in 1 file:

• src/dr/evolution/tree: TreeTraitProvider.java (+8)

rambaut 2011-09-08 11:10 Rev.: 4289

Started to implement continuous traits in BEAUti. Needed extensive cleaning up and streamlining of code.

1 lines of code changed in 1 file:

• src/dr/evolution/tree: FlexibleTree.java (+1)

rambaut 2011-07-28 00:04 Rev.: 4124

Fix for issue 468: http://code.google.com/p/beast-mcmc/issues/detail?id=468

2 lines of code changed in 1 file:

• src/dr/evolution/tree: Tree.java (+2)

msuchard 2011-06-16 04:29 Rev.: 4028

Adding TreeAnnonator parsing ability for MarkovJumps processes with multiple sites. To be used in Markov-modulated substitution models with Chris Simon.

16 lines of code changed in 1 file:

• src/dr/evolution/tree: TreeTrait.java (+16 -1)

msuchard 2011-05-08 02:04 Rev.: 3970

Fixed starting state bug (was using Math.double random variable)

2 lines of code changed in 2 files:

• src/dr/evolution/tree: MutableTree.java (new)

msuchard 2011-04-27 15:50 Rev.: 3962

Added logging ability for complete substitution history under uniformization; there is a high likelihood that I broke some of the Markov jumps/reward mechanisms in this update.

1 lines of code changed in 1 file:

• src/dr/evolution/tree: TreeTrait.java (+1 -1)

alexei.drummond 2011-03-15 09:15 Rev.: 3874

20 taxa, 7 constraints, 0.1seconds

16 lines of code changed in 2 files:

• src/dr/evolution/tree: CountConstrainedRankedHistories.java (+16 -7)

alexei.drummond 2011-03-14 22:08 Rev.: 3873

yes

228 lines of code changed in 3 files:

• src/dr/evolution/tree: CountConstrainedRankedHistories.java (+212 -32), RankedNode.java (+16 -7)

alexei.drummond 2011-03-14 15:32 Rev.: 3871

count constrained ranked trees

231 lines of code changed in 1 file:

• src/dr/evolution/tree: CountConstrainedRankedHistories.java (+231)

alexei.drummond 2011-03-12 17:59 Rev.: 3870

ranked forest

48 lines of code changed in 3 files:

• src/dr/evolution/tree: RankedForest.java (new), RankedNode.java (+19 -12)

alexei.drummond 2011-03-12 15:39 Rev.: 3869

ranked forest

361 lines of code changed in 2 files:

• src/dr/evolution/tree: RankedForest.java (+73 -9), RankedNode.java (+288 -129)

alexei.drummond 2011-03-11 15:39 Rev.: 3868

325 lines of code changed in 2 files:

• src/dr/evolution/tree: RankedForest.java (+98), RankedNode.java (+227)

dong.w.xie 2011-02-15 09:08 Rev.: 3796

Trunk: big change of new Tracer, and this check-in starts using List instead array in Variate.

6 lines of code changed in 2 files:

• src/dr/evolution/tree: LineageCountThroughTime.java (new)

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>

26 lines of code changed in 3 files:

• src/dr/evolution/tree: NodeRef.java (new), Tree.java (+25)

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

automatic intelliJ minor syntax fixes

5 lines of code changed in 2 files:

• src/dr/evolution/tree: TreeShape.java (+5 -5)

rambaut 2010-10-08 21:16 Rev.: 3620

Decoupled the process of checking node heights are within bounds to confirm that an operator is correct from using it to reject a move. By default tree moves just call treeModel.endTreeEdit() to finish editing the tree. If they need to check whether the resulting tree is valid they can call checkTreeIsValid() which throws an exception if not. Most moves do not need this check if correctly implemented. Some I wasn't too sure about so I left the check in for those to give the same behaviour (but it is up to the operator whether this check is made and what to do about it).

TreeModel.endTreeEdit() can optionally make this test (switch on a flag at the top of TreeModel) but throws a runtimeException so stops the program if it fails.

43 lines of code changed in 3 files:

• src/dr/evolution/tree: MutableTree.java (+4 -4), SubtreeSlide.java (+39 -47)

rambaut 2010-09-11 01:58 Rev.: 3526

Fixed an issue with UPGMA producing zero internal branch lengths and causing zero probability in some tree priors.

4 lines of code changed in 1 file:

• src/dr/evolution/tree: MutableTree.java (+4 -1)

msuchard 2010-07-14 09:00 Rev.: 3309

Cleaning up dN/dS summary statistics and adding TreeTraits for flu backbone

192 lines of code changed in 3 files:

• src/dr/evolution/tree: Tree.java (+33), TreeNodeFilter.java (new 36), TreeTrait.java (+123 -2)

msuchard 2010-06-24 03:52 Rev.: 3281

Modifying CodonPartitionedRobustCounting to differentiate between internal and external branches; minor optimization of uniformized state history simulation

34 lines of code changed in 1 file:

• src/dr/evolution/tree: TreeTrait.java (+34 -11)

msuchard 2010-06-17 10:45 Rev.: 3273

Critical fix: branch rates now print out in tree log under new TreeTrait framework. Also starting to remove duplicated code from classes needing to output different combinations of TreeTrait summaries

153 lines of code changed in 3 files:

• src/dr/evolution/tree: Tree.java (+1 -1), TreeTrait.java (+149 -19), TreeTraitProvider.java (+3)

msuchard 2010-06-16 13:54 Rev.: 3271

Add several wrappers to convert automatically between different reductions of TreeTraits (sum over tree, sum across sites, etc.). One can even double-wrap to get sum over tree + sum across sites. This should reduce substantial code-duplication and earn me a gold star.

172 lines of code changed in 1 file:

• src/dr/evolution/tree: TreeTrait.java (+172 -7)

rambaut 2010-06-07 23:07 Rev.: 3235

Simplified TreeTrait interface to remove explicit dimensionality. If multidimensional traits are required then it needs to use double[] as the type.

90 lines of code changed in 2 files:

• src/dr/evolution/tree: Tree.java (+15 -14), TreeTrait.java (+75 -61)

msuchard 2010-06-06 04:51 Rev.: 3229

Added an ascertainment correction unit test.

2 lines of code changed in 1 file:

• src/dr/evolution/tree: TreeTrait.java (+2 -2)

rambaut 2010-06-05 02:18 Rev.: 3224

Fixed TreeTrait to deal with a null trait value array (for example from the root of a tree).

30 lines of code changed in 2 files:

• src/dr/evolution/tree: Tree.java (+24 -22), TreeTrait.java (+6)

dong.w.xie 2010-06-04 15:56 Rev.: 3222

TRUNK: beauti: more for user-specified starting tree.

14 lines of code changed in 1 file:

• src/dr/evolution/tree: Tree.java (+14)

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