March 2008 Commit Log

Number of Commits:
37
Number of Active Developers:
6
rambaut 2008-03-30 22:06 Rev.: 797

Removed a dependency on some classes in dr.math on the "Parameter" class in dr.inference. The MultivariateDistribution was taking a Parameter as an argument but then extracting the values immediately. Just moved this up to the calling class MultivariateDistributionLikelihood

108 lines of code changed in 8 files:

alexander.alekseyenko 2008-03-29 22:36 Rev.: 793

Fixed a small bug in sclatedTreeLengthRateModel.
Made stuff for ALS model more generic.
Created a default prior for ALS model and a class that integrates over the acquisition rate. Modified the example file accordingly.

429 lines of code changed in 8 files:

rambaut 2008-03-29 05:11 Rev.: 792

Added an error Logger (set up in BEAST main) to which numerical errors during the run of the MCMC can be logged (for example CoalesentLikelihood now logs NaNs and Infinities returned from the likelihood calculator. By default, a Servere error will terminate the run but the new -errors command line option can introduct the maximum number of such errors to tolerate. Warnings can also be written for debugging purposes. Here is how to write to it:

Logger.getLogger("error").severe("CoalescentLikelihood is " + Double.toString(lnL));

121 lines of code changed in 5 files:

rambaut 2008-03-29 05:06 Rev.: 791

As I threatened, I have now deleted dr.app.beastdev (I had one yes and no complaints).

9 lines of code changed in 6 files:

rambaut 2008-03-28 23:02 Rev.: 790

A bit more cleaning up. AbstractCoalescentLikelihood is now called OldAbstractCoalescentLikelihood to indicate to authors of descendent classes that they may wish to try and use the new "AbstractCoalescentLikelihood" which is cleaner and more modular. It also allows for <include> and <exclude> of taxon lists to do subtrees. Basically, all subclasses have to do is implement calculateLogLikelihood() and call getIntervals() and getTree() to get the current intervals and tree objects. See "CoalescentLikelihood" for an example (also the parser for including and excluding taxon lists - otherwise provide nulls).

992 lines of code changed in 13 files:

jheled 2008-03-28 18:17 Rev.: 789

I assume this was somehow left out of the update

1 lines of code changed in 1 file:

alexander.alekseyenko 2008-03-28 14:47 Rev.: 788

Beast was crushing when logging nodeHeightParameters because individual
Node.heightParameters.id == null. Modified Node constructor to set the id to Node's number in the owning Tree.

1 lines of code changed in 1 file:

rambaut 2008-03-28 04:09 Rev.: 786

Added the "include" and "exclude" options to CoalescentLikelihood that previously were only available in CoalescentMRCALikelihood which resulted in duplication of code.

42 lines of code changed in 2 files:

rambaut 2008-03-28 01:49 Rev.: 785

I have renamed 'NewCoalescentLikelihood' as 'CoalescentLikelihood' to clarify things a bit. NewCoalescentLikelihood was more efficient and clean implementation and it's parser was installed as the default 'coalescentLikelihood' anyway since BEAST v1.4.x.

I have renamed 'CoalescentLikelihood' to AbstractCoalescentLikelihood and removed the parser (made it abstract). This class is used as a base by a number of other classes (i.e., BayesianSkylineLikelihood). I guess that ideally, we see what of AbstractCoalescentLikelihood the descendents actually use and strip out some of it.

1402 lines of code changed in 14 files:

alexander.alekseyenko 2008-03-27 11:46 Rev.: 784

Added classes necessary for MSSD a.k.a. Aquisition-Loss-Substitution (ALS) a.k.a. Immigration-Mutation-Death model functionality. Added prior and integrated immigration prior correction for alternative splicing creation and loss model.
AscertainedSitePatterns -- can handle ascertainment of two types
MutationDeathType -- extends a datatype with an additional state for the death state. Slightly differently (more clean?) structured than the other datatypes in the project. Let me know if you like it.
MutationDeathModel -- extends an arbitrary SubstitutionModel to include an additional absorbing death state.
ScaledTreeLengthRateModel -- Scales the sum of all edges to a specified value (like 1.0 in my case)

testBinary.xml -- a small example of who all of this stuff work
Changes:
BeastParser: added the parsers here
SitePatterns: made comparePatterns() protected instead of private
FrequencyModel: added a function to get the frequency parameter

2142 lines of code changed in 15 files:

bloomquist 2008-03-26 05:51 Rev.: 782

Changed remaining skyline's to skyride's to match up with Minin et al. resubmission.

636 lines of code changed in 7 files:

bloomquist 2008-03-26 05:47 Rev.: 781

Renamed GMRFSkylineLikelihood to GMRFSkyrideLikelihood to match up with Minin et al. resubmission.

741 lines of code changed in 7 files:

rambaut 2008-03-26 03:22 Rev.: 780

An error in the BeastParser - some parsers were included twice

4 lines of code changed in 3 files:

bloomquist 2008-03-23 05:59 Rev.: 779

Made significant run-time improvements to GMRFSkylineLikelihood and GMRFSkylineBlockUpdateOperator. Run-time cut by 0.5 - 0.333.

559 lines of code changed in 2 files:

msuchard 2008-03-22 09:26 Rev.: 778

Hacked a check-point into AncestralStateTreeLikelihood.calculationLikelihood() to make sure that AbstractSubstitutionModel is returning a valid eigen-decomposition. The diagonalization routines in ASM break-down for even slightly ill-conditioned matrices of large size.

42 lines of code changed in 3 files:

rambaut 2008-03-22 03:07 Rev.: 777

Added an Exponential-Logistic model. Compiles but not tested

370 lines of code changed in 4 files:

rambaut 2008-03-22 00:12

Fixed an error in TreeAnnotator when it was trying to find the modal value of a discrete trait.

35 lines of code changed in 2 files:

rambaut 2008-03-21 04:24 Rev.: 773

Updated dr.app.beast.BeastParser to contain all the parsers in dr.app.beastdev.*. Will delete dr.app.beastdev.* soon. Moved BeastMC3 across. Fixed a bug setting BSP group count in Beauti.

890 lines of code changed in 8 files:

rambaut 2008-03-21 02:59 Rev.: 772

Added 'AttributePatternsParser' which uses attributes attached to the taxa in a taxon list to construct a pattern.

109 lines of code changed in 2 files:

rambaut 2008-03-20 04:23 Rev.: 770

Upgraded commons-math library to v1.2. This now provides a numerical integrator which I have set DemographicFunction to use if required (instead of the simple embedded function that was there before).

84 lines of code changed in 3 files:

rambaut 2008-03-20 03:13 Rev.: 769

Fix for the Transmission History model.

1 lines of code changed in 2 files:

rambaut 2008-03-20 02:11 Rev.: 768

Fixed TreeAnnotator (now uses considerably less memory at the expense of reading the trees 3 times). Can now annotate very large trees.

31 lines of code changed in 3 files:

msuchard 2008-03-19 20:43 Rev.: 767

Added AncestralSequenceAnnotator (which is a rip-off of TreeAnnotator). This class takes output from BAli-Phy and resample/summarizes the internal node sequences (including indels). Sorry, but I had to add a new constructor to TreeModel that copies the tree attributes.

3130 lines of code changed in 11 files:

Sebastian.Hoehna 2008-03-14 15:44 Rev.: 761

Added a parameter for convinience to set the credible set

18 lines of code changed in 2 files:

Sebastian.Hoehna 2008-03-14 15:43 Rev.: 760

added some parts so that the CladeMetric works

5 lines of code changed in 1 file:

Sebastian.Hoehna 2008-03-14 15:38 Rev.: 759

Added the entry for the missing SubtreeSlide Operator.

1 lines of code changed in 1 file:

rambaut 2008-03-14 12:52 Rev.: 758

Updated version (build number)

1 lines of code changed in 1 file:

rambaut 2008-03-14 12:03 Rev.: 757

More tweaks for DNA damage model (possibly working now)

9 lines of code changed in 1 file:

rambaut 2008-03-14 11:43 Rev.: 756

Fixes for DNA damage model

133 lines of code changed in 3 files:

rambaut 2008-03-14 10:29 Rev.: 755

Fixes for DNA damage model

189 lines of code changed in 4 files:

rambaut 2008-03-14 09:50 Rev.: 754

Fixes for DNA damage model

3 lines of code changed in 3 files:

rambaut 2008-03-14 05:55 Rev.: 753

Implemented a model of DNA damage

639 lines of code changed in 4 files:

rambaut 2008-03-12 01:44 Rev.: 752

Updated the JEBL jar in /lib

0 lines of code changed in 1 file:

rambaut 2008-03-12 01:35 Rev.: 751

Fixed the ANT build files to use 'jebl.jar' which is up to date. Should fix some compile problems.

3 lines of code changed in 3 files:

rambaut 2008-03-11 12:36 Rev.: 750

Fixed an issue with TracerApp not running on non-Mac OSs

17 lines of code changed in 1 file:

rambaut 2008-03-11 00:25 Rev.: 748

Added the ability to set an initial value to traits at nodes in TreeModel; Improved TreeAnnotator to use considerably less memory by making 3 passes of the tree file instead of 2; A few fixes to TreeStat to make it compile again.

1682 lines of code changed in 8 files:

rambaut 2008-03-01 23:47 Rev.: 740

Allowed Tracer to read scientific notation for the state number (to allow it to read Lamarc files). Now gives the line number if there is an inconsistent state spacing.

100 lines of code changed in 3 files:

February 2008 »

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