structure
(5 files, 770 lines)
[root]/src/dr/evolution/coalescent
structure
(5 files, 770 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 137 (100.0%) | 3292 (100.0%) | 24.0 |
| rambaut | 43 (31.4%) | 1480 (45.0%) | 34.4 |
| alexei.drummond | 13 (9.5%) | 791 (24.0%) | 60.8 |
| jheled | 71 (51.8%) | 661 (20.1%) | 9.3 |
| msuchard | 4 (2.9%) | 335 (10.2%) | 83.7 |
| bloomquist | 3 (2.2%) | 17 (0.5%) | 5.6 |
| dong.w.xie | 2 (1.5%) | 5 (0.2%) | 2.5 |
| mandevsgill | 1 (0.7%) | 3 (0.1%) | 3.0 |
BEAUti now generates a hierarchical coalescent simulator that generates monophyletic groups and required clade heights. Clade heights can be given in the Taxon Sets table in the column called 'age'. These should lie inside any hard prior bounds (this is not done automatically).
2 lines of code changed in 2 files:
Fixed a (hopefully) final issue with sampling dates.
2 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.
3 lines of code changed in 1 file:
uncommitting an erroneous revision
0 lines of code changed in 4 files:
Trunk new Trace: more corrections to use 2d ArrayList ArrayList<ArrayList> not List[].
5 lines of code changed in 2 files:
Improved store/restore functionality in GMRF multilocus model.
27 lines of code changed in 2 files:
GMRF multilocus likelihood appears to compute properly; operators still do not work and there is debugging material to remove.
3 lines of code changed in 1 file:
Started work with Mandev on multilociGMRF
271 lines of code changed in 1 file:
Started work on multilocus GMRF Skyride
37 lines of code changed in 1 file:
Updated getInverseIntensity() so that when growthRate = 0, it matches up with getIntensity().
4 lines of code changed in 2 files:
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:
Minor correction of intercapitalization.
22 lines of code changed in 4 files:
math 2.0 package name
3 lines of code changed in 2 files:
comments changes
1 lines of code changed in 2 files:
intellij auto
3 lines of code changed in 3 files:
snapshot my latest version just in case
3 lines of code changed in 2 files:
Refactoring to remove illegal dependencies. No classes in dr.evolution.* packages should depend on classes in dr.evomodel.* or dr.inference.* or dr.evomodelxml. Also converted dr.evolution.coalescent.IntervalType to enum and minor other tidy ups.
29 lines of code changed in 2 files:
move MultiLociTreeSet out of dr.evolution
0 lines of code changed in 1 file:
code police
7 lines of code changed in 1 file:
A small improvment in reducing usage of litteral string constants.
Each constant should be defined in one place and referenced elsewhere.
The best place I found is in the various parsers. This may be wrong but now moving it elsewhere is a simple matter.
1 lines of code changed in 1 file:
Continued development of the Traits panel
8 lines of code changed in 1 file:
Added an alternative parameterization of PiecewiseExponential that has a vector of pop sizes and a final ancestral growth rate. This should help with mixing (having a vector of growth rates was problematic because of the interaction between adjacent rates).
129 lines of code changed in 1 file:
automatic code improvments (intellij)
2 lines of code changed in 1 file:
Rearranged the check for difficult intervals to avoid a divide by zero when intervalArea is zero.
2 lines of code changed in 1 file:
Added a 'getThreshold' method to the DemographicFunction which gets passed on to the calculate likelihood function. This defaults to zero in DemographicFunction. Abstract but is 1E-12 in VDdemographicFunction.
13 lines of code changed in 1 file:
Added an optional 'threshold' on the static method 'calculateLogLikelihood' to allow for a check for ill-conditioned coalescent intervals. A static method with the old signature calls this with a zero threshold (i.e., no check). This just moves the problem up to CoalescentLikelihood which calls this static method.
11 lines of code changed in 1 file:
Removed an (underflow?) check in calculating the coalescent likelihood. This was preventing a big initial tree from being calculated. The warning message is still going to be written to see if there is a long term problem.
9 lines of code changed in 1 file:
Added a 'DemographicLogger' - this is a logger for recording reconstructions (popsizes + change points) for skyline, skyride type models. The logger takes a class that implements 'DemographicReconstructor' interface. For BSPs this is the BayesianSkylineLikelihood itself.
The actual reconstruction has not been implemented for BSP yet.
Added an Exponential-growth BSP model.
146 lines of code changed in 3 files:
Added a piecewise-exponential growth model.
198 lines of code changed in 1 file:
Code Police
1 lines of code changed in 2 files:
Comments, nitpicking
2 lines of code changed in 1 file:
code nitpicking
1 lines of code changed in 2 files:
improved speed by factor of 8 by using binary search and caching intensities, and added ability to do multiple replicates.
233 lines of code changed in 3 files:
Add handling of constant intervals in Piecewise linear. Those can happen demographic is explicitly set for simulation purposes.
17 lines of code changed in 1 file:
build script and usage instructions for Variable Coalescent Simulator version 0.1
1 lines of code changed in 1 file:
fixed bone-headed intensity and inverse-intensity functions. The previous functions were piecewise-constant with population size being set to the mean over the interval! This is now properly piecewise linear.
12 lines of code changed in 1 file:
Added 5'th optional argument - file name to log the demographic
42 lines of code changed in 1 file:
simulation of trees from piecewise linear populations
245 lines of code changed in 2 files:
Fixes to ExponentialLogistic
10 lines of code changed in 4 files:
Some progress. Now creates a set of 'mu' parameters across all active partition models. The current stumbling block is that the deltaExchange operator requires the weight of each partition. This is currently supposed to be provided by 'BeautiOptions.getActivePartitionWeights()' but I haven't finished implementing it yet.
112 lines of code changed in 1 file:
(33 more)