Lines of Code
[root]/src/dr/evomodelxml/speciation
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 113 (100.0%) | 3345 (100.0%) | 29.6 |
| graham853@gmail.com | 40 (35.4%) | 1547 (46.2%) | 38.6 |
| dong.w.xie | 35 (31.0%) | 1220 (36.5%) | 34.8 |
| alexei.drummond | 10 (8.8%) | 188 (5.6%) | 18.8 |
| jheled | 7 (6.2%) | 156 (4.7%) | 22.2 |
| rambaut | 14 (12.4%) | 125 (3.7%) | 8.9 |
| msuchard | 2 (1.8%) | 72 (2.2%) | 36.0 |
| jheled@gmail.com | 3 (2.7%) | 30 (0.9%) | 10.0 |
| dong.w.xie@gmail.com | 2 (1.8%) | 7 (0.2%) | 3.5 |
Allopolyploid model. Added diploidRootIsRoot flag (but only tested code when true), changed formula for network prior, added error check relating to oneHybridization flag, improved debug output.
AlloppChangeNumHybridizations: added error check relating to oneHybridization flag.
AlloppChangeNumHybridizationsParser: added error relating to oneHybridization flag.
AlloppDiploidHistory.java: nicer debug output, changes for diploidRootIsRoot flag.
AlloppLeggedTree: simpler debug output.
AlloppMulLabTree: nicer debug output.
AlloppNetworkNodeSlide: Changed operateOneNodeInDiploidHistory() for diploidRootIsRoot flag.
AlloppNetworkPrior: Changed formula for prior (9.0 -> 7.0*sqrt(#diploids))
AlloppSpeciesBindings: nicer debug output.
AlloppSpeciesNetworkModel: changes for diploidRootIsRoot flag, debug output.
AlloppSpeciesNetworkModelParser: changes for diploidRootIsRoot flag.
9 lines of code changed in 2 files:
Allopolyploid model. Added MCMC operator to flip legs and sequences of tetraploid tree to improve mixing. Improved sampling for initial state of network. Added statistic for number of hybridizations.
59 lines of code changed in 1 file:
Allopolyploid model: adding code for arbitrary numbers of diploids, tetraploids, hybridizations.
150 lines of code changed in 3 files:
trunk: merge Issue 656 : fix p=0 in Birth Death Serial Sampling Model, and update Unit tests.
7 lines of code changed in 2 files:
Porting fixes from 1.7.3 back into the trunk
0 lines of code changed in 10 files:
Code for n diploids, one hybridization now working. Experimental code (PopsIO) added for multispecies coalescent with population size parameters integrated out.
356 lines of code changed in 14 files:
Adding multiply-labelled tree model. MulSpeciesTreeModel, MulMSCoalescent, MulSpeciesBindings, MulSpeciesTreePrior. Operators MulTreeNodeSlide, MulTreeSequenceReassignment. Plus parsers.
Minor updates to AlloppSpeciesBindings, AlloppSpeciesNetworkModel, the latter dues to changes in logging behaviour.
331 lines of code changed in 4 files:
Minor text edit.
2 lines of code changed in 2 files:
trunk:solve Issue 562: BEAUTi : Birth Death Epidemiology Model update
1 lines of code changed in 1 file:
New parameterization of Tanja's BDSSM for epidemiology
17 lines of code changed in 1 file:
New parameterization of Tanja's BDSSM for epidemiology
106 lines of code changed in 1 file:
trunk: some fixes of Issue 556: BEAUti "birth-death serially sampled model" correction required
3 lines of code changed in 1 file:
trunk: finish calibrated Yule, but may have bugs.
1 lines of code changed in 2 files:
improve enum CorrectionType to suit for BEAUti, and finish Calibrated Yule GUI part, but need further work on xml generator.
5 lines of code changed in 1 file:
Allopolyploid model: Made code compatible with Java 1.5 (removed @Override's). Added citation. More sensible implementation of debugging logger.
5 lines of code changed in 9 files:
637 lines of code changed in 7 files:
trunk: I think Issue 463 is solved, but cannot test because of Issue 485
2 lines of code changed in 1 file:
Add an alternative exact marginal
11 lines of code changed in 1 file:
Trunk: fix BEAUti BDSS part
6 lines of code changed in 1 file:
parser fix
4 lines of code changed in 2 files:
more fixes to calibration code
6 lines of code changed in 1 file:
Tidied up parsers and added option to specify epoch widths from the origin rather than the tips.
8 lines of code changed in 2 files:
likelihoods correct! phew! Late night debugging with Denise and Tanja in Zurich ;-)
131 lines of code changed in 1 file:
removed final time interval
8 lines of code changed in 1 file:
Add first version for exact marginal for the general case of N monophyletic clades
13 lines of code changed in 1 file:
Trunk: add log transformation into BDSS
10 lines of code changed in 1 file:
Re-organize calibration code. add experimental "approximate" marginal.
15 lines of code changed in 1 file:
add all worked out closed form calibration marginals: parent of clade, two nested clades, clade and root.
66 lines of code changed in 1 file:
Trunk: fix another trick bug of BDSS
7 lines of code changed in 1 file:
Trunk: fix a bug of BDSS parser, and correct attribute name
8 lines of code changed in 1 file:
Attempting to standardize citations in BEAUti for a more professional look; am unclear why we did not stick with the Citable interface.
2 lines of code changed in 1 file:
Trunk: A new XML for Calibration with Yule.
7 lines of code changed in 1 file:
Trunk: finish Brith Death Serial Sampling in BEAUti, but some of xmls are not running.
2 lines of code changed in 1 file:
Trunk: start to implement Brith Death Serial Sampling in BEAUti.
30 lines of code changed in 3 files:
Trunk: fix test and parser of MA
1 lines of code changed in 2 files:
Trunk: initial research on Model Averaging
103 lines of code changed in 1 file:
Add chs, log and exp tp RPN calculator
Add Tree height statistic parser tp .properties
Special calibration cases use RPN expression.
40 lines of code changed in 1 file:
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
7 lines of code changed in 1 file:
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>
28 lines of code changed in 3 files:
Added the sampling of the origin of the infection to the birth-death serial sampling model.
9 lines of code changed in 1 file:
(9 more)