May 2013 Commit Log

Number of Commits:
35
Number of Active Developers:
8
mdhall272@gmail.com 2013-05-17 04:53 Rev.: 5656

Bug fix

0 lines of code changed in 2 files:

rambaut 2013-05-16 08:25 Rev.: 5655

Fixed issue with creating leaf height parameters for multiple trees but the XML is not going to work. Probably need to disallow this in BEAUti.

0 lines of code changed in 2 files:

rambaut 2013-05-16 07:54 Rev.: 5654

Leaf taxa are only added to a treeModel if it has them.

27 lines of code changed in 3 files:

mandevsgill 2013-05-16 07:51 Rev.: 5653

A few more minor changes (essentially all operations involving meanCache and storedMeanCache now done by cacheHelper). Rewritten code does not break anything.

0 lines of code changed in 2 files:

rambaut 2013-05-16 07:43 Rev.: 5652

Origin date needs its units set.

0 lines of code changed in 2 files:

mdhall272@gmail.com 2013-05-16 02:58 Rev.: 5651

More comments

0 lines of code changed in 4 files:

mdhall272@gmail.com 2013-05-16 02:54 Rev.: 5650

Minor fixes and comment changes

18 lines of code changed in 4 files:

mandevsgill 2013-05-14 17:55 Rev.: 5649

Some very minor changes

160 lines of code changed in 1 file:

rambaut 2013-05-13 04:17 Rev.: 5648

Auto sets the size of the MarkovJump count register

28 lines of code changed in 4 files:

rambaut 2013-05-13 04:13 Rev.: 5647

Added fasta (and fa and fas) as recognized extensions

2 lines of code changed in 2 files:

rambaut 2013-05-11 17:33 Rev.: 5646

Fixed that BEAUti was putting stateTagName attribute into TreeLikelihood elements (even though they should only be there for ancestralStateTreeLikelihoods). Was giving a parser warning when run (no other consequences).

11 lines of code changed in 5 files:

mandevsgill 2013-05-11 05:09 Rev.: 5645

Starting on diffusion with drift

5 lines of code changed in 2 files:

rambaut 2013-05-11 02:10 Rev.: 5644

Added tool tip for lambda tree signal parameter check box.

18 lines of code changed in 6 files:

rambaut 2013-05-10 22:32 Rev.: 5643

BEAUti: added Pagel's Lambda transform of tree shape to measure phylogenetic signal in continuous traits. Check box in sites panel for continuous trait partition. Lambda appears in priors table and operators table.

101 lines of code changed in 7 files:

rambaut 2013-05-10 03:29 Rev.: 5642

Added parsing and setting of date precisions in BEAUti plus generation of uniform sampling within these bounds. Also fixed the date calculations so Jan 1st (say 2013) is 2013.0.

260 lines of code changed in 17 files:

julia.pal.r@gmail.com 2013-05-09 05:42 Rev.: 5641

Latest version with new operator for joint--TODO: let Parameters.restore for vectors with different sizes. Tracer analysis doesn't read log files with {num,num,..}

1186 lines of code changed in 10 files:

msuchard 2013-05-09 01:55 Rev.: 5640

Fixing TreeTransform applied to EmpiricalTreeDistribution (again)

6 lines of code changed in 6 files:

mdhall272@gmail.com 2013-05-09 00:22 Rev.: 5639

efficiency improvements & other misc small fixes

24 lines of code changed in 7 files:

msuchard 2013-05-08 07:20 Rev.: 5638

Incorrectly delegated getBranchLength() such that no transformation was occurring.

17 lines of code changed in 5 files:

msuchard 2013-05-08 04:03 Rev.: 5637

Updated MultivariateTraitTree to work with EmpiricalTreeDistribution

10 lines of code changed in 5 files:

mdhall272@gmail.com 2013-05-07 23:10 Rev.: 5636

With the option -calculaterates this will now calculate mean Q matrix entries for all supported rates and give this in the text and KML files. Please test.

453 lines of code changed in 1 file:

msuchard 2013-05-07 07:43 Rev.: 5635

Fixing transformed trees when random

404 lines of code changed in 21 files:

fbielejec 2013-05-07 02:44 Rev.: 5634

simulate under implemented models only

102 lines of code changed in 12 files:

fbielejec 2013-05-07 01:46 Rev.: 5633

create demo models

48 lines of code changed in 1 file:

fbielejec 2013-05-07 01:06 Rev.: 5632

adding demography models

879 lines of code changed in 18 files:

msuchard 2013-05-06 15:27 Rev.: 5631

Finally interfacing multivariate traits, although they are now generally integrated out.

265 lines of code changed in 17 files:

rambaut 2013-05-03 10:29 Rev.: 5630

Improved tip date parsing - now can read variable precision dates.

17 lines of code changed in 1 file:

rambaut 2013-05-03 10:07 Rev.: 5629

Added local root search to Pathogen.

140 lines of code changed in 4 files:

msuchard 2013-05-03 07:25 Rev.: 5628

Fixed log determine of a matrix and positive-definite check in WishartDistribution; there is still an error in LUPDecomposition.isPD()

21 lines of code changed in 6 files:

rambaut 2013-05-03 02:58 Rev.: 5627

A couple of minor fixes to the main(). -version now works. -beagle_info on the command line doesn't throw up the options dialog but prints the info and quits.

2 lines of code changed in 2 files:

mdhall272@gmail.com 2013-05-03 02:53 Rev.: 5626

Added simpler outbreak class (no latent periods).

616 lines of code changed in 4 files:

mdhall272@gmail.com 2013-05-02 00:45 Rev.: 5625

Now fairly confident geographical analysis has to be done in post-processing - removed.

13 lines of code changed in 2 files:

gcybis@yahoo.com.br 2013-05-01 19:07 Rev.: 5624

Latent Liability model

595 lines of code changed in 2 files:

tbcbedford@gmail.com 2013-05-01 06:26 Rev.: 5623

Small correction, not working yet.

5 lines of code changed in 2 files:

tbcbedford@gmail.com 2013-05-01 05:35 Rev.: 5622

My attempt to get discreteTraitBranchRateModel working. It's almost there. However, the function:
int state = ((int[])trait.getTrait(tree, node))[traitIndex];
on line 386 is causing problems.

If getProcessValues is forced to an array of {1.0, 1.0} in getRawBranchRate then the MCMC proceeds as expected. However, if the return value of getProcessValues is set to {1.0, 1.0} then the problem persists.

58 lines of code changed in 1 file:

April 2013 »

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