tracer: doWork in EBSP needs to be reviewed, it seems a copy of BSP.
14 lines of code changed in 5 files:
trunk: merge Issue 677
124 lines of code changed in 14 files:
Missed correction.
17 lines of code changed in 2 files:
trunk: merge Issue 677 : Using Microsatellite loci for inferring one phylogenetic tree that uses all the loci.
126 lines of code changed in 13 files:
working on main menu bar
178 lines of code changed in 8 files:
Remove old version of the operator.
0 lines of code changed in 1 file:
Refactoring.
396 lines of code changed in 1 file:
Added option to specify the number of iterations using the initial covariance.
66 lines of code changed in 1 file:
Fixed citation error.
1 lines of code changed in 2 files:
Fixed typo.
1 lines of code changed in 2 files:
Working as intended. All classes necessary for TT=TMRCA model (sans geography) now complete.
3 lines of code changed in 1 file:
Cleaning up (fixing SVN tree conflict?)
32 lines of code changed in 1 file:
Cleaning up
3 lines of code changed in 2 files:
Porting typo fix from 1.7
6 lines of code changed in 2 files:
Cleaning up.
11 lines of code changed in 1 file:
Remaining part of an adaptive Metropolis (AM) algorithm/operator. Seems to be working but needs more testing. Also needs a rewrite to exploit symmetry and avoid redundant calculations.
156 lines of code changed in 1 file:
Added method to check transmission network makes sense
27 lines of code changed in 2 files:
Parser done
62 lines of code changed in 2 files:
Operator wrapping a phylogenetic tree operator that changes transmission tree accordingly (TT=TMRCA only). Still needs testing and parser.
98 lines of code changed in 2 files:
get the save paths right
35 lines of code changed in 4 files:
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.
173 lines of code changed in 22 files:
had to manually repair org.virion.jam imports to fix ant build problem
25 lines of code changed in 10 files:
Modify to handle ambiguity.
3 lines of code changed in 2 files:
updated buildfile
5 lines of code changed in 1 file:
updated buildfile
125 lines of code changed in 4 files:
cleaning up
1583 lines of code changed in 9 files:
Display taxa height
11 lines of code changed in 5 files:
Display taxa height
455 lines of code changed in 4 files:
First part of an adaptive Metropolis (AM) algorithm/operator.
290 lines of code changed in 1 file:
Generate for multiple trees option done. Some extra error checking.
144 lines of code changed in 6 files:
ProductStatistics now take the ID of the relevant XML object as a name if they do not otherwise have one (so the relevant columns in the log file and hence in Tracer will not simply be called "productStatistic"). This is how SumStatistic already works.
9 lines of code changed in 2 files:
aligned radio buttons with GridBagConstraints
31 lines of code changed in 2 files:
working on simulating from multiple trees
186 lines of code changed in 6 files:
working on simulating from multiple trees
302 lines of code changed in 7 files:
Retrospectively added a couple of bug fixes to the version list for completeness.
3 lines of code changed in 2 files:
Keep Colt flag off unless shown to provide more reliable simulants.
7 lines of code changed in 2 files:
Merging version stuff and copyright dates with 1.7 branch.
80 lines of code changed in 22 files:
- nextGamma(alpha, lambda) in Colt needs to be called with 1/scale instead of scale
- also replaced log(x/scale) by log(x) - log(scale) to avoid numerical errors when evaluating very small values from a gamma distribution
23 lines of code changed in 1 file:
generate number of simulations fasta files
334 lines of code changed in 4 files:
Ported recent updates from 1.7 branch
7 lines of code changed in 2 files:
Ported recent updates from 1.7 branch
27 lines of code changed in 5 files:
Erroneous import giving a warning in Hudson
0 lines of code changed in 2 files:
Efficiency savings
11 lines of code changed in 2 files:
Efficiency savings
56 lines of code changed in 1 file:
Updating parser list to match.
2 lines of code changed in 1 file:
New case and case set classes with likelihood functions borrowed from Morelli et al, PLoS Comp Biol, 2012
597 lines of code changed in 6 files:
text message changes for the renaissance counting method in AncestralStatesOptionsPanel
8 lines of code changed in 2 files:
Tree model element and idrefs now set. XML generation almost done
228 lines of code changed in 3 files:
First version of an independent sampler from a normal distribution model.
177 lines of code changed in 1 file:
Forgot to include the actual parameter in the XML rules.
8 lines of code changed in 2 files:
fixed a bug in frequency model editor
2 lines of code changed in 1 file:
Set idrefs for xml elements. Need to rewrite the tree model element with a more elegant solution
368 lines of code changed in 3 files:
Set idrefs for clock model
55 lines of code changed in 3 files:
write model only if unique. Moving to idrefs
154 lines of code changed in 2 files:
Implemented bounds and negative offsets for empirical distributions; improved normalization.
9 lines of code changed in 2 files:
Side-stepping trouble with Gamma RV generation
16 lines of code changed in 1 file:
add only unique taxa to the list
65 lines of code changed in 5 files:
Operator reporting and citation fix.
5 lines of code changed in 1 file:
direct call to updateUI not needed
6 lines of code changed in 3 files:
taxa list updates call taxa table model to repaint table. This fixes previous problem
38 lines of code changed in 4 files:
First version of an independent sampler from a gamma distribution.
164 lines of code changed in 2 files:
BSS gui allows for multiple trees now. Problems with taxa panel not getting updated
155 lines of code changed in 5 files:
Porting changes from 1.7
32 lines of code changed in 3 files:
BEAUti generates coalescent trees with matching opening and closing tags, a good property to have.
30 lines of code changed in 1 file:
Proposed solution for handling multiple ambiguity codes in stochastic Dollo BEAUti generator
4 lines of code changed in 2 files: