randomlocalmodel
(4 files, 42 lines)
[root]/src/dr/evomodel/tree
randomlocalmodel
(4 files, 42 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 410 (100.0%) | 21834 (100.0%) | 53.2 |
| alexei.drummond | 77 (18.8%) | 7296 (33.4%) | 94.7 |
| msuchard | 85 (20.7%) | 6421 (29.4%) | 75.5 |
| rambaut | 108 (26.3%) | 4548 (20.8%) | 42.1 |
| bloomquist | 16 (3.9%) | 1386 (6.3%) | 86.6 |
| jheled | 58 (14.1%) | 750 (3.4%) | 12.9 |
| aaron.darling | 4 (1.0%) | 742 (3.4%) | 185.5 |
| akaruiws | 6 (1.5%) | 257 (1.2%) | 42.8 |
| Sebastian.Hoehna | 6 (1.5%) | 190 (0.9%) | 31.6 |
| baele.guy@gmail.com | 2 (0.5%) | 82 (0.4%) | 41.0 |
| Michael.DefoinPLatel | 3 (0.7%) | 60 (0.3%) | 20.0 |
| Sibon.Li@gmail.com | 4 (1.0%) | 59 (0.3%) | 14.7 |
| dong.w.xie | 39 (9.5%) | 32 (0.1%) | 0.8 |
| alexander.alekseyenko | 2 (0.5%) | 11 (0.1%) | 5.5 |
Fixing TreeTransform applied to EmpiricalTreeDistribution (again)
6 lines of code changed in 6 files:
Incorrectly delegated getBranchLength() such that no transformation was occurring.
17 lines of code changed in 5 files:
Updated MultivariateTraitTree to work with EmpiricalTreeDistribution
10 lines of code changed in 3 files:
Fixing transformed trees when random
249 lines of code changed in 2 files:
Finally interfacing multivariate traits, although they are now generally integrated out.
64 lines of code changed in 2 files:
New version of an additional method to copy a proposed tree into the current treeModel.
19 lines of code changed in 1 file:
First version of an additional method to copy a proposed tree (for example, from the coalescentSimulator) into the current treeModel. At the moment, copying rates and traits is not yet implemented. These may need to be copied during a separate tree traversal, if the direct access to leftChild and rightChild cannot be circumvented ...
63 lines of code changed in 1 file:
Created an 'AttributeBranchRateModel' which exposes an attribute embedded in a tree as a branch rate model.
2 lines of code changed in 2 files:
Temporarily removed EmpricialTrees implementation of BranchRateModel as it was confusing the TreeLikelihood parser (which picked it up as the first BranchRateModel even when it is not being used as such).
3 lines of code changed in 1 file:
EmpiricalTreeDistributionModel can now read a rate attribute and expose it as a branchRateModel (it now implements that interface).
64 lines of code changed in 1 file:
Missed correction.
17 lines of code changed in 2 files:
Porting fixes for issue http://code.google.com/p/beast-mcmc/issues/detail?id=671 to trunk.
18 lines of code changed in 2 files:
Added unit-IntervalLatentLiabilityLikelihood for VNTRs; plan to refactor to remove duplicated code once more fully tested.
11 lines of code changed in 1 file:
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.
4 lines of code changed in 1 file:
Overhauled the date system so that the 'height' timescale is now universal to all taxa. Previously there was an issue if you create independent trees on different taxon sets, they would have their own 'zero' point depending on their most recently sampled taxon. Now, when you call 'setDate' for a taxon (as done by the TaxonParser) it keeps track of the globally most recent sample (in a static variable) and can give the global height from a given date object using a static function. Taxon objects also have a 'getHeight' methods that uses this system. The two main sources of trees (CoalescentSimulator and NewickParser) now use these heights (simplifying their own code). Runs benchmarks correctly but keep an eye out for issues.
2 lines of code changed in 1 file:
On second thought, it might just be easier to group several TreeParameterModels together. Committing just to keep a record.
82 lines of code changed in 5 files:
Generifying TreeParameterModel to handle multiple data-types (double, double[], int, etc.). Also base abstract class supports an includeTips flag developed in TrialTreeParameterModel (now depricated). NewTreeParameterModel should replace TreeParameterModel after extensive testing.
434 lines of code changed in 3 files:
TreeTransforms are now loggable as branch traits
66 lines of code changed in 3 files:
Fixed store/restore functionality of BetaDistributionModel
26 lines of code changed in 1 file:
Fixed error last revision introduced into TreeParameterModel
1 lines of code changed in 1 file:
Introduced a trial TreeParameterModel that excludes external branches; created a new branch-specific Pagel estimator
152 lines of code changed in 3 files:
Trying a tree transform
90 lines of code changed in 3 files:
Refactoring TransformedTree to make generalizations easier
137 lines of code changed in 3 files:
Implementing transformed trees and Pagel's lambda estimator
89 lines of code changed in 1 file:
Improved ability to co-opt an existing root height in StarTreeModel
25 lines of code changed in 2 files:
Added ability to co-opt an existing root height in StarTreeModel
29 lines of code changed in 1 file:
Reverting accidental change
1 lines of code changed in 1 file:
Keeping source Java 1.5 compatible.
4 lines of code changed in 1 file:
Started to implement ancestral state reconstruction at a node.
11 lines of code changed in 2 files:
Ported sequence error models to BeagleTreeLikelihood and implemented a variant model that emits tip states rather than tip partials.
13 lines of code changed in 2 files:
Loggers weren't logging if they overrode the base class log(int state) - because it had been changed to log(long state). Put a final int version in the base class to prevent overriding.
7 lines of code changed in 9 files:
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).
0 lines of code changed in 1 file:
Upgraded chain length to a 64 bit integer so that chain lengths > 2.1 billion can be done. This addresses issue 540. Runs OK, accepts long chain lengths but not actually tested a run of > 2.1 billion.
4 lines of code changed in 4 files:
Skeleton for Gaussian Process coalescent model
1 lines of code changed in 1 file:
Better way to handle star trees via a derived TreeModel
128 lines of code changed in 1 file:
Preliminary star tree implementation as an alternative to the correlated trait models; would function better as a subclass of TreeModel than TreeLikelihood.
35 lines of code changed in 1 file:
Fixed a few issues with TreeEvents being fired inappropriately. Also updates to AntigenicTreeLikelihood.
2 lines of code changed in 2 files:
After some more extensive testing, I have now removed the node heights bound check as default. Certain moves still may make this check.
1 lines of code changed in 1 file:
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.
13 lines of code changed in 1 file:
Whilst I test the consequence of removing the height bound checking in TreeModel.endTreeEdit(), I have reinstated the test but it now throws a RuntimeException to see if any operators rely on this test failing to check for invalid moves.
9 lines of code changed in 1 file:
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