January 2012 Commit Log

Number of Commits:
52
Number of Active Developers:
6
fbielejec 2012-01-31 22:54 Rev.: 4619

imma spaghetti coder

235 lines of code changed in 1 file:

fbielejec 2012-01-31 00:15 Rev.: 4618

more comments

11 lines of code changed in 1 file:

fbielejec 2012-01-30 23:59 Rev.: 4617

simplified the logic

54 lines of code changed in 1 file:

fbielejec 2012-01-30 07:27 Rev.: 4616

correcting for some other situations

109 lines of code changed in 1 file:

fbielejec 2012-01-30 05:45 Rev.: 4615

sequential code

84 lines of code changed in 1 file:

fbielejec 2012-01-29 09:17 Rev.: 4614

working on more then two matrices case

102 lines of code changed in 1 file:

tbcbedford@gmail.com 2012-01-26 05:27 Rev.: 4613

I cleaned up some things and moved to a proportional framework. S, I and R are now 0 to 1 and sum to 1. There is an additional host population size parameter that scales each of these proportions. I use a delta exchange operator on the proportions.

Also, I fixed most of the mixing issues in a (stupidly) trivial fashion. I had assumed that smaller scaleFactors result in smaller operations. Starting scaleFactors off at 0.99 for recoveryRate and reproductiveNumber fixes most everything.

53 lines of code changed in 3 files:

msuchard 2012-01-25 07:14 Rev.: 4612

Reverting accidental change

1 lines of code changed in 1 file:

msuchard 2012-01-25 07:07 Rev.: 4611

Keeping source Java 1.5 compatible.

263 lines of code changed in 2 files:

tbcbedford@gmail.com 2012-01-25 04:00 Rev.: 4610

Some cleanup of time keeping.

66 lines of code changed in 3 files:

tbcbedford@gmail.com 2012-01-25 03:45 Rev.: 4609

Streamlining Timeseries Statistics.

27 lines of code changed in 1 file:

fbielejec 2012-01-24 08:48 Rev.: 4608

ugly but works, just like me

57 lines of code changed in 1 file:

julia.pal.r@gmail.com 2012-01-24 05:37 Rev.: 4607

updating Likelihood

20 lines of code changed in 1 file:

tbcbedford@gmail.com 2012-01-24 04:06 Rev.: 4606

Rather than a custom logger, I've switched to statistics that describe time series. Have separate statistics for susceptibles, infecteds, recovereds and effective population size through time. Need to implement user-defined ranges and step sizes in the XML.

107 lines of code changed in 3 files:

fbielejec 2012-01-24 03:28 Rev.: 4605

commented out a parser

1 lines of code changed in 1 file:

fbielejec 2012-01-24 03:25 Rev.: 4604

fixed small bug

3 lines of code changed in 1 file:

tbcbedford@gmail.com 2012-01-24 02:41 Rev.: 4603

Starting to implement a time series logger.

284 lines of code changed in 3 files:

tbcbedford@gmail.com 2012-01-24 02:03 Rev.: 4602

Reparameterized transmission rate to R0. This allows me to put a lower limit of 1.0 on R0. Appears to working with simulated data. Need to assume a value on recovery rate for identifiability. Still getting poor acceptance probabilites. However, have had success with an operator that scales S, I and R simultaneously.

scale(sir.reproductiveNumber) 0.0036
scale(sir.susceptibles) 0.0099
scale(sir.infecteds) 0.1221
scale(sir.recovereds) 0.0106
up:sir.susceptibles sir.infecteds sir.recovereds down: 0.3145

35 lines of code changed in 4 files:

tbcbedford@gmail.com 2012-01-23 23:50 Rev.: 4601

I had moved this to forward time. It didn't work very well at all. Too difficult to choose good initial parameter values. Switch back to backward time. Now working on multivariate operators.

70 lines of code changed in 5 files:

graham853@gmail.com 2012-01-23 01:15 Rev.: 4600

Improved MCMC moves for allopolyploid model (diploid root, moves of legs).

234 lines of code changed in 4 files:

julia.pal.r@gmail.com 2012-01-22 16:22 Rev.: 4599

updating

24 lines of code changed in 1 file:

julia.pal.r@gmail.com 2012-01-21 15:41 Rev.: 4598

Commented changes - still revising

124 lines of code changed in 2 files:

tbcbedford@gmail.com 2012-01-21 01:26 Rev.: 4597

Rolling back SIRModel likelihood.

1 lines of code changed in 1 file:

tbcbedford@gmail.com 2012-01-21 00:31 Rev.: 4596

Convergence issues had been an identifiability problem. Was going to an initial state with non-zero recovereds. I fixed this here by adding a likelihood to the model that prefers zero recovereds. However, this is causing massively slow mixing, because changing any one of the epidemiological parameters pushes the initial recovereds off their mark. Will attempt to move to a forward-simulation approach.

99 lines of code changed in 1 file:

fbielejec 2012-01-20 09:42 Rev.: 4595

minor changes

63 lines of code changed in 1 file:

fbielejec 2012-01-20 09:41 Rev.: 4594

sort epoch times

38 lines of code changed in 1 file:

tbcbedford@gmail.com 2012-01-19 05:00 Rev.: 4593

Fixed issue with initial state. However, now there seems to be convergence issues.

44 lines of code changed in 3 files:

tbcbedford@gmail.com 2012-01-19 02:15 Rev.: 4592

Identified bug in DynamicalVariable reset. Everything looks more-or-less in order. Testing now.

16 lines of code changed in 3 files:

tbcbedford@gmail.com 2012-01-19 01:29 Rev.: 4591

I've implemented store/restore in DynamicalSystem and called this from SIRModel. No longer having errors, but something is still wrong.

117 lines of code changed in 4 files:

tbcbedford@gmail.com 2012-01-18 23:21 Rev.: 4590

Streamlined Variable and Force constructors in DynamicalSystem. Interfaced SIRModel with DynamicalSystem. Doing just-in-time extension of timeseries when getValue is called. Compiles and runs, but gives a state-not-restored-correctly error.

164 lines of code changed in 3 files:

fbielejec 2012-01-18 10:04 Rev.: 4589

new buffer helper

1 lines of code changed in 1 file:

fbielejec 2012-01-18 09:20 Rev.: 4588

recompiled beagle.jar

0 lines of code changed in 1 file:

fbielejec 2012-01-18 09:20 Rev.: 4587

Beagle epoch model parser

5 lines of code changed in 1 file:

fbielejec 2012-01-18 09:20

pass BufferIndexHelper to updateTransitionMatrices

47 lines of code changed in 2 files:

fbielejec 2012-01-18 09:20 Rev.: 4584

the meat of Beagle epoch model

507 lines of code changed in 1 file:

fbielejec 2012-01-18 09:20 Rev.: 4583

pass BufferIndexHelper to updateTransitionMatrices

37 lines of code changed in 1 file:

fbielejec 2012-01-18 09:20 Rev.: 4582

new buffer helper

76 lines of code changed in 1 file:

fbielejec 2012-01-18 09:20 Rev.: 4581

getBranchIndex signature

2 lines of code changed in 1 file:

fbielejec 2012-01-18 09:19 Rev.: 4580

helper that knows everything

59 lines of code changed in 1 file:

fbielejec 2012-01-18 09:19 Rev.: 4579

parser for Beagle epoch model

89 lines of code changed in 1 file:

tbcbedford@gmail.com 2012-01-18 03:33 Rev.: 4578

Implemented linear interpolation for getValue and trapezoidal rule for getIntegral.

71 lines of code changed in 2 files:

tbcbedford@gmail.com 2012-01-18 00:58 Rev.: 4577

Implemented helper classes for dynamical systems. This is designed to simulate partial differential system via the simple Euler method. After forward calculation, can ask for the value at any point in time via fast binary search.

236 lines of code changed in 6 files:

rambaut 2012-01-17 23:38 Rev.: 4576

MJTL and ASTL now only take a substitution model as an option (they will extract it from the site model if not given).

9 lines of code changed in 2 files:

tbcbedford@gmail.com 2012-01-17 01:51 Rev.: 4575

Updated skeleton of SIRModel. Includes S, I and R parameters and doesn't crash. Returns dummy likelihood.

93 lines of code changed in 3 files:

msuchard 2012-01-13 05:14 Rev.: 4574

Adding interface for epoch models using BEAGLE

318 lines of code changed in 7 files:

rambaut 2012-01-11 01:03 Rev.: 4573

Updated BeastMC3 copyright message (uses BeastVersion now).

5 lines of code changed in 1 file:

msuchard 2012-01-10 02:55 Rev.: 4572

Adding a CnCs counting class

856 lines of code changed in 8 files:

graham853@gmail.com 2012-01-09 23:59 Rev.: 4571

Adding multiply-labelled tree model. MulSpeciesTreeModel, MulMSCoalescent, MulSpeciesBindings, MulSpeciesTreePrior. Operators MulTreeNodeSlide, MulTreeSequenceReassignment. Plus parsers.

Minor updates to AlloppSpeciesBindings, AlloppSpeciesNetworkModel, the latter dues to changes in logging behaviour.

3530 lines of code changed in 15 files:

msuchard 2012-01-05 06:26 Rev.: 4570

Modified EB Poisson smoother for sampling distribution

52 lines of code changed in 1 file:

rambaut 2012-01-04 02:27 Rev.: 4569

Implemented saving and loading of 'BEAUti' files using Java Serialization. Seems to work but complex models are not yet tested.

176 lines of code changed in 35 files:

rambaut 2012-01-04 01:03 Rev.: 4568

Cleaned up the interface for selecting starting trees.

1 lines of code changed in 1 file:

rambaut 2012-01-03 23:14 Rev.: 4567

Cleaned up the interface for selecting starting trees.

123 lines of code changed in 2 files:

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