operators
(6 files, 371 lines)
[root]/src/dr/evomodelxml/coalescent
operators
(6 files, 371 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 75 (100.0%) | 3766 (100.0%) | 50.2 |
| dong.w.xie | 42 (56.0%) | 2825 (75.0%) | 67.2 |
| julia.pal.r@gmail.com | 13 (17.3%) | 376 (10.0%) | 28.9 |
| msuchard | 6 (8.0%) | 321 (8.5%) | 53.5 |
| rambaut | 7 (9.3%) | 179 (4.8%) | 25.5 |
| mandevsgill | 2 (2.7%) | 44 (1.2%) | 22.0 |
| jheled | 3 (4.0%) | 16 (0.4%) | 5.3 |
| dong.w.xie@gmail.com | 2 (2.7%) | 5 (0.1%) | 2.5 |
working on summary - need to calculate "sigmoidal" medians, etc
1 lines of code changed in 2 files:
added the "tracer" analysis similar to EBSP
116 lines of code changed in 3 files:
Special logger
11 lines of code changed in 1 file:
Parameterizing a lot and changes in number of latents, location of latents..need to fix GP sampling of one point, problem with "last" neighbor
59 lines of code changed in 1 file:
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).
20 lines of code changed in 2 files:
Created a new cleaner coalescent simulator parser to help generate nested subtrees from taxon sets. Updating BEAUti to generate simulated trees that conform to monophyly constrants and hard bounds on tmrcas.
98 lines of code changed in 1 file:
The 'rootHeight' option had been crippled in the Coalescent Simulator preventing easy rescaling of the root height to fit constraints.
0 lines of code changed in 2 files:
delete import
0 lines of code changed in 1 file:
Updating Likelihood, need to add the GMRF part
41 lines of code changed in 1 file:
trunk: merge Issue 86: Missing validation in BayesianSkylineLikelihoodParser
5 lines of code changed in 2 files:
updating small changes in operators and adding lambda_parameter
31 lines of code changed in 1 file:
Commented changes - still revising
2 lines of code changed in 1 file:
Editing mainly GPSLikelihoodParser
76 lines of code changed in 1 file:
test
39 lines of code changed in 1 file:
Skeleton for Gaussian Process coalescent model
226 lines of code changed in 1 file:
Fixed optional parameter settings in GMRFSkyrideLikelihoodParser
1 lines of code changed in 2 files:
Updated the multilocus gmrf model so that we have a proper prior. Still needs to be cleaned up a little bit.
12 lines of code changed in 1 file:
Multilocus GMRF model has been updated and appears to be working properly. Old GMRF model should still work with the old xml syntax.
32 lines of code changed in 1 file:
Fix one bug in constrained generation of initial trees. bug was due to creation on 1 taxon tree with height 0.
4 lines of code changed in 1 file:
Trunk: merge issue 403.
3 lines of code changed in 1 file:
Made logging of multilocus GMRF skyride more convenient for plotting in Tracer:
<log id="skyrideLog" logEvery="5000" fileName="multilocusGMRF-skyride.log">
<parameter idref="skyride.logPopSize"/>
<gmrfHeightsStatistic id="skyride.intervalHeights">
<gmrfSkyrideLikelihood idref="skyrideCoalescent"/>
</gmrfHeightsStatistic>
</log>
48 lines of code changed in 1 file:
Removed duplicated code in GMRFMultilocusSkyrideLikelihood and added option in GMRFSkyride to not scale by rootHeight; turning this latter option off is for debugging only
6 lines of code changed in 1 file:
LoggerParser uses a special function to get the log file which may set different paths (for example to a working directory). Thus just checking that fileName exists may not work. So moved the check for existing file into XMLParser.getFilePrintWriter(). This has the added benefit that all loggers use this function and thus all have the overwriting behaviour.
Also added a check box to the BEAST options dialog box.
0 lines of code changed in 1 file:
Started work on multilocus GMRF Skyride
40 lines of code changed in 1 file:
Add an option to dump all demographics to a file
12 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).
61 lines of code changed in 1 file:
Trunk refactoring: fix a bug of duplcation parser name in GMRF Skyride Likelihood.
1 lines of code changed in 1 file:
Trunk refactoring: finish indel (split parsers).
9 lines of code changed in 2 files:
Trunk refactoring: finish GMRF (split parsers).
358 lines of code changed in 4 files:
Trunk refactoring: finish Logger (split parsers).
0 lines of code changed in 1 file:
Trunk refactoring: finish Likelihoods (split parsers)..
193 lines of code changed in 2 files:
Trunk refactoring: organize tree and treelikelihood parsers.
1 lines of code changed in 1 file:
Trunk refactoring: finish speciation (split parsers)..
2 lines of code changed in 2 files:
Trunk refactoring: finish coalescent (split parsers).
1046 lines of code changed in 12 files:
Trunk refactoring: 2nd part of coalescent (split parsers).
116 lines of code changed in 3 files:
Trunk refactoring: 1st part of coalescent (split parsers).
1096 lines of code changed in 13 files: