[root]/src/dr/evomodelxml
MSSD
(6 files, 289 lines)
branchratemodel
(14 files, 501 lines)
clock
(2 files, 149 lines)
coalescent
(35 files, 1879 lines)
operators
(6 files, 371 lines)
indel
(3 files, 164 lines)
operators
(28 files, 1050 lines)
sitemodel
(7 files, 388 lines)
speciation
(35 files, 1088 lines)
substmodel
(29 files, 1965 lines)
tree
(27 files, 962 lines)
treelikelihood
(7 files, 29 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 156 (100.0%) | 4920 (100.0%) | 31.5 |
| dong.w.xie | 69 (44.2%) | 1527 (31.0%) | 22.1 |
| alexei.drummond | 20 (12.8%) | 1315 (26.7%) | 65.7 |
| rambaut | 23 (14.7%) | 894 (18.2%) | 38.8 |
| Sibon.Li@gmail.com | 7 (4.5%) | 374 (7.6%) | 53.4 |
| akaruiws | 9 (5.8%) | 309 (6.3%) | 34.3 |
| alexander.alekseyenko | 3 (1.9%) | 217 (4.4%) | 72.3 |
| msuchard | 3 (1.9%) | 141 (2.9%) | 47.0 |
| jheled | 21 (13.5%) | 137 (2.8%) | 6.5 |
| bloomquist | 1 (0.6%) | 6 (0.1%) | 6.0 |
Created an 'AttributeBranchRateModel' which exposes an attribute embedded in a tree as a branch rate model.
1 lines of code changed in 2 files:
EmpiricalTreeDistributionModel can now read a rate attribute and expose it as a branchRateModel (it now implements that interface).
9 lines of code changed in 1 file:
Extract leaf traits from the compound parameter constructed in an integrated continuous trait likelihood
89 lines of code changed in 1 file:
Added command line option '-prefix <PREFIX>' to specify a string which will be prefixed to all output log files. This is an alternative to changing the log file names in the XML when running multiple replicate runs in the same location.
81 lines of code changed in 2 files:
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).
1 lines of code changed in 2 files:
Trunk refactoring: finish trace (split parsers).
158 lines of code changed in 1 file:
Fixed my last commit
0 lines of code changed in 1 file:
Modified MixtureModelBranchRates to not have to take in quantiles
124 lines of code changed in 1 file:
Trunk refactoring: organize tree and treelikelihood parsers.
0 lines of code changed in 4 files:
Trunk refactoring: finish Random Local Yule Model (split parsers).
0 lines of code changed in 3 files:
Trunk refactoring: branch rate and clock rate model (split parsers).
0 lines of code changed in 3 files:
Trunk refactoring: make evoxml parsers more organized.
12 lines of code changed in 3 files:
Trunk refactoring: make subst parsers more organized.
0 lines of code changed in 20 files:
Trunk: fix bugs, parser should return the exact model type referred.
5 lines of code changed in 3 files:
Trunk: fix BinaryCovarionModelParser bug.
1 lines of code changed in 1 file:
Trunk refactoring: complex substitution model (split parsers).
230 lines of code changed in 2 files:
Trunk refactoring: finish substitution model (split parsers).
315 lines of code changed in 4 files:
Trunk refactoring: big part of substitution model (split parsers).
402 lines of code changed in 10 files:
Trunk refactoring: substitution model - binary (spilt parsers).
345 lines of code changed in 5 files:
Added parser for Tanja's birth-death serial sampling model
97 lines of code changed in 1 file:
Added work in progress to discretizedBranchRates to allow for normalising of the mean branch rate (does not yet work properly but does not effect existing operations)
17 lines of code changed in 1 file:
Removed normalised mean rate function of TreeLogger
10 lines of code changed in 1 file:
Trunk: merge from branch 1.5 in
1 lines of code changed in 1 file:
Uploaded two new relaxed clock implementations/models, RandomDiscretizedBranchRates and MixtureModelBranchRates.
218 lines of code changed in 2 files:
Attacking the wandering taxon problem
48 lines of code changed in 1 file:
Added a metropolisHastings option to the EmpiricalTreeDistributionOperator
7 lines of code changed in 2 files:
Solve Issue 227: Fix BeastDoc to generate tag doc for BEAST users, but need enhancement.
1 lines of code changed in 1 file:
Implemented an empirical tree distribution model and operator.
5 lines of code changed in 1 file:
Implemented an empirical tree distribution model and operator.
180 lines of code changed in 3 files:
add conditional on root for yule
4 lines of code changed in 1 file:
Remove deprecated class Yule (superceeded by birth death)
Add option for conditioning on root height.
20 lines of code changed in 2 files:
added parsers for Lewis' Mk model with totaly ordered/unordered/custom ordered states.
151 lines of code changed in 1 file:
Fix the pathogen build
6 lines of code changed in 1 file:
Updated figtreepanel
3 lines of code changed in 1 file:
TreeModel that draws a random tree from a set loaded from NEXUS file.
104 lines of code changed in 1 file:
Class naming police...
217 lines of code changed in 2 files:
Biased multivariate diffusion for Oli; tweaks to tree attributes.
4 lines of code changed in 1 file:
Methods added so that when running BEAST, detail of microsatellite model and its paramters are printed to stardard out.
1 lines of code changed in 1 file:
Implementation of MicrosatelliteSamplterTreeLikelihoodParser.
0 lines of code changed in 1 file:
Parser for MicrosatelliteSamplerTreeModel.
0 lines of code changed in 1 file:
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