more DnDsPerSiteAnalysis debugging
35 lines of code changed in 1 file:
adding DnDsPerSiteAnalysis parser to development parser list
4 lines of code changed in 1 file:
TRUNK: follow-up Issue 310 to include beagle.jar in beast.jar for 1.6.0 pre.
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debugging DnDsPerSiteAnalysis
32 lines of code changed in 1 file:
adding a trace analysis for N and S counts
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Two goals acheived. (1) RobustCounting now provides per site counts to a log file and (2) example of using a helper class to log traits from a TraitProvider, will remove substantial duplicated code from CPRC and MJBTL
324 lines of code changed in 8 files:
Fixed feature in jittering continuous traits that only appeared to be fabricating data when really missing
19 lines of code changed in 2 files:
Fixed bug in ascertainment correction (miscounted) and implemented in BEAGLE. Genomic-wide SNPs here we come!
99 lines of code changed in 7 files:
Started to implement a branch rate model that takes a realization of a discrete location provided by a MarkovJumpsTreeLikelihood and produces a continuous diffusion rate based on the proportion of time spent in each location and a vector of relative rates and indicators. Builds but not finished implementing.
93 lines of code changed in 2 files:
Maintaining functional compatibility between ASTL and ASBTL. Need to figure out how to ditch one.
411 lines of code changed in 13 files:
TRUNK: revert Issue 310 and create ANT to generate beast-beagle-all.jar which includes beast.jar and default main class
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TRUNK: solve Issue 310: beast-beagle.jar not include beast.jar and no default main class
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adding "tree" and "alignment" strings to output
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the jitter method now updates non-missing values in traits only
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the jitter method now ignores traits with a missing value in any dimension
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Adding backbone to local clock model.
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Can now simulate sequences under a branch-specific substitution model; for example, different dN/dS per branch.
160 lines of code changed in 6 files:
Parameters can now be randomized at initialization; good for starting from overdispersed states and for simulation studies:
<beast>
<parameter id="test1" dimension="2">
<randomize>
<normalDistributionModel>
<mean> -5 </mean>
<precision> 1.0 </precision> </normalDistributionModel>
</randomize>
</parameter>
<parameter id="test2" value="1 2 3 4"/>
<report>
<parameter idref="test1"/>
</report>
<report>
<parameter idref="test2"/>
</report>
</beast>
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Keeping AncestralState(Beagle)TreeLikelihoods up-to-date
115 lines of code changed in 2 files:
Accidentally deleted OldTreesPanel.
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Tweak to the hypermutant model
55 lines of code changed in 3 files:
Preparing MarkovJumps to compute null distributions for tests of selection using just nucleotide models (fast, fast, fast)
435 lines of code changed in 9 files:
Daniel found a more stable dynamic rescaling -- add a makeDirty()
6 lines of code changed in 1 file:
Fixed an issue with root optimization for some trees in PathOGen.
847 lines of code changed in 15 files:
test case for Yule with one "reference" calibration
0 lines of code changed in 1 file:
TRUNK: merge Issue 307: BEAUti missing .txt in tree log using EBSP
4 lines of code changed in 1 file:
Added ability to drag and drop files into the file table of LogCombiner and the input file box of TreeAnnotator.
44 lines of code changed in 2 files:
Better solution for dynamic scaling; still need to find bug (?)
6 lines of code changed in 1 file:
Temporary solution for dynamic scaling; still need to find bug
13 lines of code changed in 1 file:
Already fixing bugs in ancestral reconstruction with ASRV
26 lines of code changed in 1 file:
Updating MarkovJumps and ancestral reconstruction to support across-site-rate-variation models
148 lines of code changed in 6 files: