July 2009 Commit Log

Number of Commits:
148
Number of Active Developers:
7
rambaut 2009-07-31 22:40 Rev.: 1970

Added more detail to the comments in 'beagle.h' about what is expected in the arrays passed to setPartials, setTipStates and setMatrix.

9 lines of code changed in 1 file:

dong.w.xie 2009-07-31 17:01 Rev.: 1969

XML example files generated from new BEAUTi.

6065 lines of code changed in 18 files:

jheled 2009-07-31 15:59 Rev.: 1968

automatic intelliJ

5 lines of code changed in 2 files:

jheled 2009-07-31 15:59 Rev.: 1967

remove incorrect check. Will try to find a better check later

3 lines of code changed in 1 file:

dong.w.xie 2009-07-31 14:41 Rev.: 1966

BEAUTi: fix deltaMu bug using Codon model.

30 lines of code changed in 2 files:

dong.w.xie 2009-07-31 14:05 Rev.: 1965

BEAUTi:
1) fix the bug of allPartitionData not updated;
2) fix bugs in Codon model;
3) tidy up reset().

126 lines of code changed in 10 files:

rambaut 2009-07-31 12:17 Rev.: 1964

Updated beagle.jar again.

0 lines of code changed in 1 file:

rambaut 2009-07-31 12:11 Rev.: 1963

Java implementation (GeneralBeagleImpl) now works for categories. Native BEAGLE returns NaN.

0 lines of code changed in 1 file:

rambaut 2009-07-31 11:58 Rev.: 1962

BEAST/Beagle now samples a simple (single category) model returning exactly the same sequence as normal BEAST. Multiple categories still returning NaN.

28 lines of code changed in 1 file:

rambaut 2009-07-31 10:29 Rev.: 1961

BeagleTreeLikelihood now works with testLikelihood.xml except when multiple categories are used. Work continues...

32 lines of code changed in 1 file:

msuchard 2009-07-31 09:59 Rev.: 1960

Started rescaling mechanism; should not interfere with Andrew's work

26 lines of code changed in 1 file:

msuchard 2009-07-31 09:21 Rev.: 1959

Cleared up default bandwidth for beta KDE from the literature.

16 lines of code changed in 3 files:

rambaut 2009-07-31 07:56 Rev.: 1958

beagle library update to fix build failure

1 lines of code changed in 2 files:

rambaut 2009-07-31 07:18 Rev.: 1957

beagle library update to fix build failure

0 lines of code changed in 1 file:

rambaut 2009-07-31 07:14 Rev.: 1956

The JNIWrapper now seems to work - the 'TinyTest' in BeagleFactory now reports:

BEAGLE library loaded
BEAGLE bootstrap: CPU - Success
logL = -1574.6362268149937 (PAUP logL = -1574.63623)

56 lines of code changed in 4 files:

philippe.lemey@gmail.com 2009-07-31 00:05

Tracer tweaks

87 lines of code changed in 2 files:

dong.w.xie 2009-07-30 16:55 Rev.: 1953

BEAUTi: fix bug to load NEXUS file with trees.

1 lines of code changed in 1 file:

dong.w.xie 2009-07-30 16:42 Rev.: 1952

BEAUTi: fix bug using Empirical of Codon model.

8 lines of code changed in 1 file:

dong.w.xie 2009-07-30 12:40 Rev.: 1951

BEAUTi:
1) add ploidy for *BEAST gene tree;
2) fix *BEAST xml bug;
3) tidy up writeIDREF.

211 lines of code changed in 12 files:

jheled 2009-07-30 11:42 Rev.: 1950

fix parsing

5 lines of code changed in 1 file:

msuchard 2009-07-30 03:45 Rev.: 1949

Implemented Snyder's contouring into TreeAnnotator for Phil.

5 lines of code changed in 1 file:

rambaut 2009-07-30 01:01 Rev.: 1948

Updated beagle.jar to fix build issue. This is non-functional but solves compilation issues for those not building against BEAGLE source code.

0 lines of code changed in 1 file:

rambaut 2009-07-30 00:55 Rev.: 1947

Updates to BEAST/BEAGLE. Not working yet.

12 lines of code changed in 1 file:

dong.w.xie 2009-07-29 15:46 Rev.: 1946

BEAUTi: make default setting when choose EBSP prior.

14 lines of code changed in 3 files:

dong.w.xie 2009-07-29 15:03 Rev.: 1945

BEAUTi: add message for choose Fix mean rate and comments in FixRateType.

9 lines of code changed in 2 files:

dong.w.xie 2009-07-29 14:08

BEAUTi: fix bug of coalescentLikelihood in EBSP using multi-loci

5 lines of code changed in 2 files:

dong.w.xie 2009-07-29 13:22 Rev.: 1942

add tracer.jar in Hudson build.

99 lines of code changed in 1 file:

msuchard 2009-07-29 11:48 Rev.: 1941

Started class hierarchy for 1D kernel density estimators in the hopes that John will need these.

225 lines of code changed in 2 files:

msuchard 2009-07-29 05:50 Rev.: 1940

Added leading term approximation.

16 lines of code changed in 1 file:

jheled 2009-07-29 05:38 Rev.: 1939

don't call methods which change object state in "toString"

5 lines of code changed in 1 file:

msuchard 2009-07-29 04:42 Rev.: 1938

Added a one-parameter Gamma distribution parser (a la Yang's rate model and for scaled mixtures of normals).

It would be nice to have a way to overload parsers in DistributionModelParser without having to give new names

33 lines of code changed in 4 files:

dong.w.xie 2009-07-28 19:44 Rev.: 1937

Fix the build

44 lines of code changed in 1 file:

dong.w.xie 2009-07-28 19:43 Rev.: 1936

Big Change of BEAUTI:
1) implement FixRateType containing estimate, fix mean, fix 1st partition to replace fixSubstitionRate;
2) comment out "mu" for no condon model;
3) correct *BEAST xml by adding updown operators;
4) fix bug to import NEXUS file when it contains subsititution model.

376 lines of code changed in 16 files:

msuchard 2009-07-28 11:40 Rev.: 1935

Implemented linear interpolation in EmpiricalDistributionLikelihood for use with John's problem.

84 lines of code changed in 4 files:

philippe.lemey@gmail.com 2009-07-28 10:07 Rev.: 1934

Tracer tweaks

13 lines of code changed in 1 file:

philippe.lemey@gmail.com 2009-07-28 08:32 Rev.: 1933

Tracer tweaks

25 lines of code changed in 1 file:

msuchard 2009-07-28 07:50 Rev.: 1932

Added a skeleton TreeStatistic for Philippe to play with.

111 lines of code changed in 2 files:

msuchard 2009-07-28 06:56 Rev.: 1931

Improved (some) numerical stability in UniformNodeHeightPrior by evaluating child0 and child1 and then multiplying, instead of multiplying first.

15 lines of code changed in 1 file:

msuchard 2009-07-28 03:28 Rev.: 1930

Making all three priors (marginal-polynomial [analytic="true", marginal="true" -- dont work], condition [analytic="true",marginal="false" --works for prior], and mc integration [analytic="false"] XML available.

30 lines of code changed in 1 file:

dong.w.xie 2009-07-27 18:42 Rev.: 1927

BEAUTi: correct *BEAST xml.

353 lines of code changed in 4 files:

dong.w.xie 2009-07-27 17:50 Rev.: 1926

BEAUTi: Issue 93: unstable result of Logistic + Growth Rate prior

9 lines of code changed in 1 file:

dong.w.xie 2009-07-27 17:05 Rev.: 1925

BEAUTi:
1) rename PartitionModelGenerator into SubstitutionModelGenerator;
2) correct initial root height for Logistic prior.

722 lines of code changed in 6 files:

alexei.drummond 2009-07-27 11:47 Rev.: 1924

tidy

3 lines of code changed in 1 file:

jheled 2009-07-27 11:01 Rev.: 1923

Intellij Auto changes

28 lines of code changed in 5 files:

msuchard 2009-07-27 10:32 Rev.: 1922

Small precision gain in UniformNodeHeightPrior

46 lines of code changed in 1 file:

msuchard 2009-07-27 07:24 Rev.: 1921

2D contouring now appears to work better in Java than in R (and much faster). TimeSlicer appropriately rescales the Brownian precision to give accurate inference ... the animations are going to look *awesome*.

741 lines of code changed in 7 files:

philippe.lemey@gmail.com 2009-07-26 21:43 Rev.: 1920

Tracer tweaks

19 lines of code changed in 1 file:

msuchard 2009-07-26 12:09 Rev.: 1919

Starting to clean up KML animation output

97 lines of code changed in 1 file:

msuchard 2009-07-26 09:33 Rev.: 1918

Implemented a Monte Carlo integral estimator in UniformNodeHeightPrior.

718 lines of code changed in 6 files:

msuchard 2009-07-25 12:13 Rev.: 1917

Bullet-proofing (or attempting to do so) eigen-decomposition and singular value decomposition. The Robust* classes are bug-hunting and temporary.

1641 lines of code changed in 4 files:

msuchard 2009-07-25 06:48 Rev.: 1916

Starting to generalize contouring so we can try different algorithms; examples show that R still works more reliably than dr.geo.contouring

193 lines of code changed in 5 files:

philippe.lemey@gmail.com 2009-07-24 21:37 Rev.: 1915

Tracer tweaks

7 lines of code changed in 1 file:

philippe.lemey@gmail.com 2009-07-24 21:00 Rev.: 1914

Tracer tweaks

265 lines of code changed in 1 file:

jheled 2009-07-24 17:09 Rev.: 1913

spelling mistake

2 lines of code changed in 1 file:

dong.w.xie 2009-07-24 13:48 Rev.: 1912

BEAUTi: make taxon sets available.

20 lines of code changed in 1 file:

dong.w.xie 2009-07-24 13:21 Rev.: 1911

BEAUTi: if tip dates then uncheck fix rate in Model panel.

1 lines of code changed in 1 file:

dong.w.xie 2009-07-24 12:25 Rev.: 1910

BEAUTi: fix a tree panel bug.

6 lines of code changed in 1 file:

jheled 2009-07-24 11:15 Rev.: 1909

Intellij auto changes

28 lines of code changed in 6 files:

jheled 2009-07-24 11:14

fix test failure

10 lines of code changed in 5 files:

jheled 2009-07-24 11:06 Rev.: 1906

Add types of trees to birth-death density

41 lines of code changed in 7 files:

dong.w.xie 2009-07-24 09:59 Rev.: 1905

Refactoring BEAUTi package to separate Swing with logic (components, generator, options, util).

448 lines of code changed in 6 files:

jheled 2009-07-23 20:36 Rev.: 1904

share constants via variables

11 lines of code changed in 1 file:

alexei.drummond 2009-07-23 16:15 Rev.: 1903

fixed test...

8 lines of code changed in 2 files:

dong.w.xie 2009-07-23 16:14 Rev.: 1902

BEAUTi: improve guess trait value.

11 lines of code changed in 2 files:

alexei.drummond 2009-07-23 14:02 Rev.: 1901

birth-death-serial-sampling-model testing... appears that birth-death-gernhard-08 gives wrong likelihoods. (see BirthDeathLikelihoodTest)

64 lines of code changed in 5 files:

rambaut 2009-07-22 22:50 Rev.: 1900

Spelling mistake.

3 lines of code changed in 1 file:

dong.w.xie 2009-07-22 16:52 Rev.: 1899

Update Big Change of BEAUTi: fix the bug of *BEAST XML generator.

642 lines of code changed in 12 files:

dong.w.xie 2009-07-22 11:35 Rev.: 1898

Update Big Change of BEAUTi: fix the bug of birth death in *BEAST.

273 lines of code changed in 3 files:

dong.w.xie 2009-07-22 10:45 Rev.: 1897

Add JUnit test VDdemographicFunctionTest into Hudson build.

6 lines of code changed in 1 file:

alexei.drummond 2009-07-21 22:25 Rev.: 1896

Tanja's Birth-Death-Serial-Sampling tree prior. Doesn't quite match up with BirthDeathGernhard08 likelihoods yet...

558 lines of code changed in 11 files:

alexei.drummond 2009-07-21 17:55 Rev.: 1895

birth-death-serial-sampling-model

199 lines of code changed in 2 files:

dong.w.xie 2009-07-21 16:47 Rev.: 1894

Update Big Change of BEAUTi: make *BEAST work.

94 lines of code changed in 6 files:

jheled 2009-07-21 16:40 Rev.: 1893

snapshot my latest version just in case

203 lines of code changed in 6 files:

jheled 2009-07-21 13:38 Rev.: 1892

remove done stuff from todo comment

1 lines of code changed in 1 file:

jheled 2009-07-21 13:37 Rev.: 1891

Handle zero sized intervals (possible on startup)

169 lines of code changed in 2 files:

jheled 2009-07-21 13:32 Rev.: 1890

Add constant population per branch model

43 lines of code changed in 1 file:

jheled 2009-07-21 13:26 Rev.: 1889

Intellij auto changes

35 lines of code changed in 4 files:

dong.w.xie 2009-07-21 13:08 Rev.: 1888

Update Big Change of BEAUTi:
1) use List to store treeFileName and subtreeFileName, and update MCMC panel;
2) correct EBSP xml, but still have a problem in VDAnalysis;
3) start to fix *BEAST.

166 lines of code changed in 7 files:

jheled 2009-07-21 12:17 Rev.: 1887

silly mistake

4 lines of code changed in 1 file:

jheled 2009-07-21 12:05 Rev.: 1886

Set new bounds when setting a new dimension (untested code)

29 lines of code changed in 1 file:

dong.w.xie 2009-07-21 09:52 Rev.: 1885

Update dr.inferencexml into Hudson build.

3 lines of code changed in 1 file:

alexei.drummond 2009-07-20 17:27 Rev.: 1884

EBSP parsing fix

146 lines of code changed in 7 files:

dong.w.xie 2009-07-20 16:35 Rev.: 1883

Update Big Change of BEAUTi:
1) correct branch rate generator and its parameters idref;
2) move Ploidy type for PartitionData into PartitionTreeModel, and add Ploidy type in Tree Model panel when EBSP prior is selected;
3) replace "value" by Parameters.Paser.Value;
4) correct XML for EBSP prior.

359 lines of code changed in 19 files:

dong.w.xie 2009-07-20 16:27 Rev.: 1882

Correct the compiling error of SplineInterpolatedLikelihood(fileName) in r1881.

5 lines of code changed in 1 file:

msuchard 2009-07-20 15:52 Rev.: 1881

Connecting SplineBasis and EmpiricalDistributionLikelihood so Andrew can get this all working while I am gone. And, I used Variables<Double> ... good on me!

93 lines of code changed in 5 files:

jheled 2009-07-20 15:49 Rev.: 1880

Print warning before setting the size - it is now illigal to change the size for some reason

4 lines of code changed in 1 file:

jheled 2009-07-20 07:47 Rev.: 1879

IntelliJ warnings

10 lines of code changed in 2 files:

jheled 2009-07-20 07:43 Rev.: 1878

Add minimum support (in #trees units) to print out for cases where 95% set is large.

55 lines of code changed in 4 files:

jheled 2009-07-20 07:41 Rev.: 1877

Species Limit statistic (debug)
Support for ploidy

100 lines of code changed in 1 file:

alexei.drummond 2009-07-19 21:50 Rev.: 1876

4 lines of code changed in 1 file:

alexei.drummond 2009-07-19 21:08 Rev.: 1875

This is the slow part: converting each model to use Variable<Double> instead of Parameter. That is why Parameter is still around. This can be done over the next X commits/months/whatever.

129 lines of code changed in 5 files:

alexei.drummond 2009-07-19 14:33 Rev.: 1874

Variable -> Parameter, Act 2.1: oops, missed a small secondary change list

420 lines of code changed in 5 files:

alexei.drummond 2009-07-19 14:30 Rev.: 1873

Parameter -> Variable, Act 2 -- this is probably the biggest change made to core BEAST in a few years. So I tagged revision 1870 for convenience. Parameter is now basically obsoleted and should be replaced by DoubleVariable or Variable<Double> where appropriate. We can now also develop some Variable<Integer> and Variable<Boolean> et cetera so should be nice in the future... I have also added a Variable<double[]> for vectors and matrices. See dr.inference.tutorial.Tutorial1 for a first peek at programmable BEAST MCMC...

2726 lines of code changed in 218 files:

alexei.drummond 2009-07-18 18:12 Rev.: 1871

First step in development of a generic version of Parameter, called Variable for now. Parameter now implements Variable<Double> but eventually all dr.inference.* will be based on Variable rather than Parameter. At least that is the idea anyway...

2009 lines of code changed in 30 files:

rambaut 2009-07-18 04:11 Rev.: 1870

Updated ANT file to include dr.inferencexml package

141 lines of code changed in 1 file:

rambaut 2009-07-18 04:01 Rev.: 1869

A few minor bits for project with John and Marc

347 lines of code changed in 4 files:

jheled 2009-07-17 16:29 Rev.: 1868

fix failure due to incorrrect parameter name
Use file chooser for save as well. Start file chooser in current directory.

65 lines of code changed in 2 files:

dong.w.xie 2009-07-17 16:06 Rev.: 1867

Update Big Change of BEAUTi:
1) make EBSP prior available for multi-data partition;
2) allow different taxa in starting tree generator;
3) some bugs fixing in branch rate generator, but it still bugs.

547 lines of code changed in 13 files:

akaruiws 2009-07-17 15:13 Rev.: 1866

23 lines of code changed in 2 files:

rambaut 2009-07-17 05:37 Rev.: 1865

Added the husk of a likelihood function that provides a density based on a (smoothed) function provided by a file of data. This is for some stuff that Marc, John and Andrew are working on. Compiles but doesn't function yet.

202 lines of code changed in 2 files:

alexei.drummond 2009-07-17 02:02 Rev.: 1864

Added a diagram outlining the *intended* top-level package structure dependencies. They are not quite realized yet -- and I don't say anything about the *intended* dependency structure within some of the large package namespaces like dr.evolution.* and dr.inference.*

0 lines of code changed in 1 file:

alexei.drummond 2009-07-17 01:13 Rev.: 1863

Beginning of refactoring to remove dr.inference.* dependency on dr.xml. Will take a while...

4062 lines of code changed in 54 files:

dong.w.xie 2009-07-16 17:15 Rev.: 1862

Update Big Change of BEAUTi:
1) fix the bug of Operator generator;
2) remove all rates into PartitionClockModelTreeModelLink;
3) comment out autocorrelated and random clock model before the release.
But there will be bugs in generator waiting regarding these changes.

237 lines of code changed in 7 files:

alexei.drummond 2009-07-15 23:53 Rev.: 1861

intellij tidy

492 lines of code changed in 18 files:

alexei.drummond 2009-07-15 16:25 Rev.: 1860

refactoring to remove illegal dependencies (dr.inference should not depend on dr.evo*.*) and tidying

3323 lines of code changed in 48 files:

dong.w.xie 2009-07-15 16:20 Rev.: 1859

Update Big Change of BEAUTi: make multi-data partition available, but there is bug in Operator Generator.

173 lines of code changed in 15 files:

jheled 2009-07-15 13:44 Rev.: 1858

comment out operator experimental code

104 lines of code changed in 8 files:

jheled 2009-07-15 13:44 Rev.: 1857

automatic intelliJ stuff

29 lines of code changed in 7 files:

jheled 2009-07-15 13:39 Rev.: 1856

31 lines of code changed in 1 file:

msuchard 2009-07-15 11:05 Rev.: 1855

Refactored MultivariateOUModel and MarginalVarianceStatistic into dr.evomodel.subst because (while neither are evolutionary related) MultivariateOUModel depends on a continuous-time Markov chain (SubstitutionModel) and MarginalVarianceStatistic depends on MultivariateOUModel.

549 lines of code changed in 6 files:

msuchard 2009-07-15 09:25 Rev.: 1854

Added some simple descriptive statistics to TimeSlicer summary.

45 lines of code changed in 1 file:

msuchard 2009-07-15 04:16 Rev.: 1853

TimeSlicer can now return 2D HPD region summaries.

239 lines of code changed in 5 files:

dong.w.xie 2009-07-14 17:05 Rev.: 1852

Fix bug of GMRF smoothed skyride model by Alexei.

42 lines of code changed in 2 files:

dong.w.xie 2009-07-14 15:15 Rev.: 1851

Update Big Change of BEAUTi: add missing operators.

30 lines of code changed in 5 files:

msuchard 2009-07-14 08:30 Rev.: 1850

Process one tree at a time to save considerable memory

135 lines of code changed in 1 file:

alexei.drummond 2009-07-13 23:56 Rev.: 1849

A short description of the top-level packages and their expected dependencies. A couple of the top-level packages do not currently conform to expected dependency relationships. Will weed this badness out in the next couple of days. If you are one of the culprits then please fix before I break your code.

70 lines of code changed in 1 file:

alexei.drummond 2009-07-13 23:44 Rev.: 1848

Refactoring tidy up. Reducing interdependencies between top-level packages. Will upload dependency guidelines to wiki soon.

3406 lines of code changed in 46 files:

alexei.drummond 2009-07-13 23:07 Rev.: 1847

Refactoring tidy up. Top level packages should not be added lightly. dr.exporters package contained a single class that was an AbstractXMLObjectParser. Added to dr.evomodelxml package.

794 lines of code changed in 5 files:

alexei.drummond 2009-07-13 22:45 Rev.: 1846

arg.. broken build #2..

6 lines of code changed in 1 file:

alexei.drummond 2009-07-13 22:31 Rev.: 1845

Refactoring to remove illegal dependencies. No classes in dr.evolution.* packages should depend on classes in dr.evomodel.* or dr.inference.* or dr.evomodelxml. Also converted dr.evolution.coalescent.IntervalType to enum and minor other tidy ups. (fixes previous broken build. oops)

372 lines of code changed in 6 files:

alexei.drummond 2009-07-13 22:26 Rev.: 1844

Refactoring to remove illegal dependencies. No classes in dr.evolution.* packages should depend on classes in dr.evomodel.* or dr.inference.* or dr.evomodelxml. Also converted dr.evolution.coalescent.IntervalType to enum and minor other tidy ups.

4491 lines of code changed in 33 files:

jheled 2009-07-13 21:49 Rev.: 1843

move MultiLociTreeSet out of dr.evolution

123 lines of code changed in 5 files:

dong.w.xie 2009-07-13 17:08 Rev.: 1842

Update Big Change of BEAUTi: fix bugs in generator and change default values. But some of operators are not showing.

96 lines of code changed in 7 files:

dong.w.xie 2009-07-13 11:15 Rev.: 1841

Update Big Change of BEAUTi: fix bug of Logistic tree prior.

1 lines of code changed in 1 file:

jheled 2009-07-12 09:24 Rev.: 1840

Seems like a critical initialization is missing

2 lines of code changed in 1 file:

alexei.drummond 2009-07-11 18:39 Rev.: 1839

Implemented NodeAttributeProvider inference for TreeParameterModel. The longer run of testAutocorrelatedRelaxedClock.xml appears to give significantly different results than the provided expectations -- but the expectations are based on a run whose lowest ESSs are only just above 100...

36 lines of code changed in 2 files:

alexei.drummond 2009-07-11 15:25 Rev.: 1838

Converted Autocorrelated Relaxed clock models to use new TreeParameterModel so that they have a similar pattern to Uncorrelated Relaxed clock models in the XML. Neither model now uses the <nodeRates> facility in TreeModel. Hopefully I haven't slowed anything down -- the test XML file suggests it gets the right answers at least!!

161 lines of code changed in 6 files:

alexei.drummond 2009-07-11 11:52 Rev.: 1837

Added a new TreeParameterModel class, that provides a parameter value associated with each node in the tree (optionally including the root) and tracks any tree changes. Retrofitted DiscretizedBranchRates and ArbitraryBranchRates with the new TreeParameterModel. I have checked that uncorrelated relaxed clocks still work correctly, but I couldn't find a test XML from ArbitraryBranchRates, so Marc Suchard should test this... Also if somebody could check I haven't inadvertantly slowed anything down that would also be good. Once I have change the autocorrelated clocks to use this framework we can remove NodeRates and NodeTraits from TreeModel! Woohoo.

268 lines of code changed in 3 files:

alexei.drummond 2009-07-10 21:45 Rev.: 1836

tidy

842 lines of code changed in 22 files:

alexei.drummond 2009-07-10 21:26 Rev.: 1835

tidy

585 lines of code changed in 9 files:

dong.w.xie 2009-07-10 16:44 Rev.: 1834

Update Big Change of BEAUTi: fix bugs in generator, but it is still wrong using Logistic Growth tree prior and UPGMA.

82 lines of code changed in 8 files:

dong.w.xie 2009-07-10 13:44 Rev.: 1833

Update Big Change of BEAUTi:
1) Add dynamic link PartitionClockModelTreeModelLink between PCM and PTM;
2) Make generator to generate xml successfully given 1 data partition.

218 lines of code changed in 7 files:

dong.w.xie 2009-07-09 17:06 Rev.: 1832

Update Big Change of BEAUTi: modify BranchRate generator.

77 lines of code changed in 5 files:

rambaut 2009-07-09 04:38 Rev.: 1831

Updated BEAST version to v1.5beta4 and build r1831

3 lines of code changed in 1 file:

rambaut 2009-07-09 03:55 Rev.: 1830

Added a parser synonym 'jeffreysPrior' for the OneOnXPrior to maintain backwards compatibility for previous XML.

4 lines of code changed in 1 file:

alexei.drummond 2009-07-08 20:39 Rev.: 1829

tweaks.

172 lines of code changed in 3 files:

dong.w.xie 2009-07-08 17:32 Rev.: 1828

Update Big Change of BEAUTi: modify generator, but BranchRate generator still has problem.

718 lines of code changed in 13 files:

alexei.drummond 2009-07-08 10:52 Rev.: 1827

Better name

149 lines of code changed in 5 files:

alexei.drummond 2009-07-08 10:48 Rev.: 1826

Renamed "JeffreysPrior" to what it actually is: an improper prior equal to Prod_i (1/x_i) for statistic x, that is in *some cases* the Jeffreys prior (e.g. for the population size parameter in constant size coalescent tree prior).

617 lines of code changed in 5 files:

msuchard 2009-07-08 07:12 Rev.: 1825

TimeSlicer now works for branch-specific rate variation models.

17 lines of code changed in 1 file:

philippe.lemey@gmail.com 2009-07-06 16:11 Rev.: 1824

Tracer tweaks

18 lines of code changed in 1 file:

alexei.drummond 2009-07-05 19:18 Rev.: 1823

tidying up some of the example files -- the eventual aim is for the tag names for id/idref pairs to always match for consistency, and enhanced ability to use standard parsing tools such as XMLSchema et cetera. At the moment I have modified XMLParser so that it just prints a warning to stderr unless strictXML is turned on, in which case an XMLParserException is thrown when the tag names of an id/idref pair don't match.

1769 lines of code changed in 19 files:

dong.w.xie 2009-07-03 15:34 Rev.: 1822

Update Big Change of BEAUTi: the part of generator.

651 lines of code changed in 19 files:

msuchard 2009-07-03 12:44 Rev.: 1821

TimeSlicer now works for multiple (and multivariate) traits and multiple time-points, plus it imputes traits with the correct noise level.

213 lines of code changed in 2 files:

msuchard 2009-07-03 07:50 Rev.: 1820

Starting a post hoc analysis program to give tree samples at slices in time. Currently used for generating density plots of angles of diffusion. Ultimately will be used to generate locations samples at arbitrary points in time (BETTER animation in GoogleEarth)

337 lines of code changed in 1 file:

dong.w.xie 2009-07-02 11:59 Rev.: 1819

Update Big Change of BEAUTi: add PloidyType for BEAUTi.

60 lines of code changed in 3 files:

dong.w.xie 2009-07-01 16:26 Rev.: 1818

Update Big Change of BEAUTi: add clock model table in Model panel

50 lines of code changed in 3 files:

dong.w.xie 2009-07-01 12:41 Rev.: 1817

Update Big Change of BEAUTi: store the links between PD, PSM, PCM, PTM, PTP in the class using their class references, List<> of them in BeautiOption is not used anymore. And use getPartition...() in BeautiOption to get the current list of PD or PSM or PCM or PTM.

655 lines of code changed in 19 files:

June 2009 »

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