Directory src/test/dr/math/

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msuchard 2011-06-19 15:55 Rev.: 4044

Added (approx.) conditional reference prior for overall substitution rate scalar into BEAUti

16 lines of code changed in 2 files:

• src/test/dr/math: ProcrustesTest.java (new)

msuchard 2011-06-19 05:46 Rev.: 4043

Fixed bug in Procrustes and added UnitTest.

102 lines of code changed in 3 files:

• src/test/dr/math: MathTestCase.java (new), ProcrustesTest.java (+95)

msuchard 2011-04-29 10:18 Rev.: 3968

Uniformized simulation now falls back on rejection sampling when numerically instable.

21 lines of code changed in 2 files:

• src/test/dr/math: UniformizedStateHistoryTest.java (new)

msuchard 2011-04-09 08:55 Rev.: 3928

Fixed numerical instability in empirical Bayes smoother for a Poisson-Gamma model

13 lines of code changed in 2 files:

• src/test/dr/math: EmpiricalBayesPoissonSmootherTest.java (+13 -1)

dong.w.xie 2011-02-15 09:08 Rev.: 3796

Trunk: big change of new Tracer, and this check-in starts using List instead array in Variate.

2 lines of code changed in 2 files:

• src/test/dr/math: KDEDistributionTest.java (+2 -3)

msuchard 2010-07-14 21:31 Rev.: 3313

JUnitTest for empirical Bayes smoother

40 lines of code changed in 1 file:

• src/test/dr/math: EmpiricalBayesPoissonSmootherTest.java (+40)

msuchard 2010-07-13 23:44 Rev.: 3306

Started work on multilocus GMRF Skyride

81 lines of code changed in 1 file:

• src/test/dr/math: KDEDistributionTest.java (+81)

msuchard 2010-05-01 10:07 Rev.: 3151

Updating MarkovJumps and ancestral reconstruction to support across-site-rate-variation models

7 lines of code changed in 1 file:

• src/test/dr/math: MathTestCase.java (+7)

msuchard 2010-04-24 06:58 Rev.: 3132

MarkovJumpsBeagleTreeLikelihood now supports all CTMC that can be uniformized (I believe this is all finite-state models).

53 lines of code changed in 1 file:

• src/test/dr/math: UniformizedStateHistoryTest.java (+53 -6)

msuchard 2010-03-27 11:58 Rev.: 3079

Completed UnitTest for simulation via Uniformization; added UniformizedSubstitutionModel to connect MarkovJumpsTreeLikelihood with the Uniformization method

42 lines of code changed in 1 file:

• src/test/dr/math: UniformizedStateHistoryTest.java (+42 -14)

msuchard 2010-03-26 11:04 Rev.: 3074

Added methods to simulate end-conditioned CTMC using the Uniformization method; this is the most optimal, simulation algorithm available and should make Stochastic Mapping and Coalescent-with-Migration models much, much faster (when real eigen decompositions are not available ... if the model is real diagonalizable MarkovJumps is still the way to go)

177 lines of code changed in 1 file:

• src/test/dr/math: UniformizedStateHistoryTest.java (+177)

msuchard 2010-03-25 13:02 Rev.: 3071

Can now simulate (and report) the complete history of any model in BEAST, most importantly codon models (with branch rate variation) and report the true number of synonymous and nonsynonymous mutations in a synthetic dataset.

8 lines of code changed in 1 file:

• src/test/dr/math: MathTestCase.java (+8)

msuchard 2010-03-25 06:23 Rev.: 3070

Further work for RobustCounting

26 lines of code changed in 3 files:

• src/test/dr/math: KroneckerOperationTest.java (+1 -2), MathTestCase.java (+25)

msuchard 2010-03-03 12:49 Rev.: 3014

Delegating funcationality in IntegratedMultivariateTraitLikelihood for profiling and future refactoring into a TraitLikelihoodCore

48 lines of code changed in 1 file:

• src/test/dr/math: KroneckerOperationTest.java (+48 -7)

msuchard 2010-02-25 09:43 Rev.: 2977

Still working on product chain models and robust counting

18 lines of code changed in 1 file:

• src/test/dr/math: KroneckerOperationTest.java (+18 -1)

msuchard 2010-02-21 08:06 Rev.: 2952

Added Kronecker product and sum operations; will be used for product chain substitution models for robust counting

100 lines of code changed in 1 file:

• src/test/dr/math: KroneckerOperationTest.java (+100)