Lines of Code
[root]/src/dr/evomodel/branchratemodel
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 226 (100.0%) | 6232 (100.0%) | 27.5 |
| rambaut | 89 (39.4%) | 2244 (36.0%) | 25.2 |
| alexei.drummond | 61 (27.0%) | 1997 (32.0%) | 32.7 |
| Sibon.Li@gmail.com | 7 (3.1%) | 819 (13.1%) | 117.0 |
| msuchard | 26 (11.5%) | 784 (12.6%) | 30.1 |
| alexander.alekseyenko | 2 (0.9%) | 153 (2.5%) | 76.5 |
| dong.w.xie | 14 (6.2%) | 83 (1.3%) | 5.9 |
| tbcbedford@gmail.com | 3 (1.3%) | 63 (1.0%) | 21.0 |
| jheled | 20 (8.8%) | 61 (1.0%) | 3.0 |
| Michael.DefoinPLatel | 2 (0.9%) | 27 (0.4%) | 13.5 |
| sibon.li | 2 (0.9%) | 1 (0.0%) | 0.5 |
Small correction, not working yet.
5 lines of code changed in 2 files:
My attempt to get discreteTraitBranchRateModel working. It's almost there. However, the function:
int state = ((int[])trait.getTrait(tree, node))[traitIndex];
on line 386 is causing problems.
If getProcessValues is forced to an array of {1.0, 1.0} in getRawBranchRate then the MCMC proceeds as expected. However, if the return value of getProcessValues is set to {1.0, 1.0} then the problem persists.
58 lines of code changed in 1 file:
DiscreteTraitBranchRateModel parser tweaks.
36 lines of code changed in 1 file:
Caching of rates doesn't seem to work with multiple partitions so turning it off now. The lazy computation of these (which does work) should prevent large overheads of computing these repeatedly at operator time (which was considerable when using gamma distributions due to the numerical quantile finding).
32 lines of code changed in 2 files:
Created an 'AttributeBranchRateModel' which exposes an attribute embedded in a tree as a branch rate model.
73 lines of code changed in 1 file:
Added caching of quantiles of rate categories and lazy computation (to avoid repeated computation of these).
22 lines of code changed in 1 file:
RandomDiscretizedBranchRates has been renamed to the more meaningful ContinuousBranchRates. RandomDiscretizedBranchRatesParser has been kept and throws an error in the unlikely case that someone actually has been using this implementation.
244 lines of code changed in 2 files:
Added skew-normal distribution model
17 lines of code changed in 2 files:
Introduced a trial TreeParameterModel that excludes external branches; created a new branch-specific Pagel estimator
8 lines of code changed in 1 file:
Fixed an issue with local clocks not propogating rates down the entire clade.
1 lines of code changed in 2 files:
Fixed caching on DTBRM
62 lines of code changed in 1 file:
Debugging DTBRM
10 lines of code changed in 1 file:
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).
19 lines of code changed in 6 files:
DiscreteTraitBranchRateModel with Markov rewards
22 lines of code changed in 1 file:
Additions to the comments.
4 lines of code changed in 1 file:
Transferring my changes from branch 1.6 to trunk:
Changes to LogNormalDistributionModel to allow for the stdev value to also not
be in log space (r3774)
Changes to UncorrelatedRelaxedClockTest due to changes in
LogNormalDistributionModel in r3774 (r3775)
Minor change in MixtureModelBranchRates to fix an issue caused by changes in
revision 3735 (r3773)
Bug fix for AncestralSequenceAnnotator plus added a window to select
input/output files (r3819)
Fixed spelling for GeneralSubstitutionModelTest (r3833)
Fixed a RuntimeException for AncestralStateTreeLikelihood (r3957)
1 lines of code changed in 2 files:
Re-implemented logging of random local clock indicators in tree log files; this ability was lost when we converted over to tree traits.
2 lines of code changed in 2 files:
Fixed a few issues with TreeEvents being fired inappropriately. Also updates to AntigenicTreeLikelihood.
1 lines of code changed in 1 file:
A specific external/internal rate model to test an idea.
130 lines of code changed in 1 file:
Removed System.out.println's from DiscretizedBranchRates
10 lines of code changed in 1 file:
Trunk: solve Issue 341: Random local clock model Bug
8 lines of code changed in 1 file:
Cleaning up dN/dS summary statistics and adding TreeTraits for flu backbone
4 lines of code changed in 1 file:
Branch rate models can now return a logDensity so that they may include the correct normalization constants.
22 lines of code changed in 2 files:
TRUNK: solve Issue 325: processValues[] in DiscreteTraitBranchRateModel should be the size of number of states NOT number of rates
29 lines of code changed in 1 file:
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
8 lines of code changed in 2 files:
Fixed store/restore of subordinated process for Uniformization; also fixed reward process for Uniformization
0 lines of code changed in 1 file:
Tweaks for checking store/restore with ancestral states and Markov processes; I still do not understand why saving the ancestral states is unnecessary.
1 lines of code changed in 1 file:
DiscreteTraitBranchRateModel now works again for ancestral state reconstructions. Something is still wrong with AncestralStateBeagleTreeLikelihood however.
34 lines of code changed in 1 file:
Added a 'backbone' local clock to LocalClockModel (sorry it took so long Philippe).
56 lines of code changed in 1 file:
Trying a reparameterization of DTBRM
1 lines of code changed in 1 file:
Additional work on DiscreteTraitBranchRateModel - adding an indicator parameter to provide link between state and rate.
11 lines of code changed in 1 file:
Trying a reparameterization of DTBRM
44 lines of code changed in 1 file:
Additional work on DiscreteTraitBranchRateModel - adding an indicator parameter to provide link between state and rate.
31 lines of code changed in 1 file:
A few tweaks
3 lines of code changed in 1 file:
Normalized the naming of a few classes and added a note in the MCMC parser to say if the fullEvaluation has been turned off.
269 lines of code changed in 2 files:
Simplified TreeTrait interface to remove explicit dimensionality. If multidimensional traits are required then it needs to use double[] as the type.
49 lines of code changed in 3 files:
Started to get DiscreteTraitRateModel working with dwell time from a MJBTL.
6 lines of code changed in 1 file:
I have abandoned dr.app.beagle.evomodel.branchratemodel.MarkovJumpsBranchRateModel and integrated that functionality into DiscreteTraitRateModel. This latter class now takes a TreeTrait which is either of the Integer type in which case it is assumed to be a node reconstruction of the state or a 'double[]' type in which case it is assumed to be a vector of dwell times for each state for each branch. I have also left the option of a parsimony reconstruction. I have also restructured things so that everything is done as dwell times - the node reconstruction variants (both likelihood and parsimony) just assume a state transition mid point on the branch. I have tried to average the parsimony variant across ambiguous state reconstructions at the nodes but I am not sure that this is a good idea (but then probably the same could be said for the whole parsimony approximation).
126 lines of code changed in 1 file:
TreeTraits commit number 2. This one is a bit more wide ranging with potential to break things. 1) BranchAttributeProvider and NodeAttributeProvider have been deleted and replaced with a combination of TreeTraits and TreeTraitProviders. Sources implement TreeTraitProvider to say that they can provide information about nodes and branches. A good example of a class which has been generalized is AncestralState (in evomodel.treelikelihood) - this now just takes a TreeTrait and logs the trait for a given MRCA (the trait can be anything at all - whereas previously it took an AncestralStateTreeLikelihood).
2 lines of code changed in 2 files:
This update does a number of things. 1) TreeLoggerParser and DemographicLoggerParser were in dr.inferencexml which breaks the dependency rules as they link to things in dr.evomodel. These are now moved to dr.evomodelxml. 2) A dr.evolution.tree.TreeTrait interface is created which is a general purpose interface for access to traits on nodes/branches. BranchAttributeProvider and NodeAttributeProvider will be replaced by this interface in the next update. 3) All BranchRateModels now have a common abstract base class AbstractBranchRateModel to implement their common features (these now implement TreeTrait to provide rates).
331 lines of code changed in 27 files:
(74 more)