Directory src/dr/math/matrixAlgebra/

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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()

15 lines of code changed in 2 files:

• src/dr/math/matrixAlgebra: LUPDecomposition.java (+15 -5)

msuchard 2013-03-27 03:48 Rev.: 5544

Implemented a log-determinant routine for numerical stability and fixed getParameterValue in DiagonalMatrix

768 lines of code changed in 3 files:

• src/dr/math/matrixAlgebra: LUPDecomposition.java (+278 -268), Matrix.java (new)

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.

1568 lines of code changed in 2 files:

• src/dr/math/matrixAlgebra: RobustEigenDecomposition.java (new 986), RobustSingularValueDecomposition.java (new 582)

jheled 2008-11-19 12:11 Rev.: 1318

Code Police

1 lines of code changed in 1 file:

• src/dr/math/matrixAlgebra: LUPDecomposition.java (+1 -2)

msuchard 2008-09-01 09:12 Rev.: 1173

ComplexeSubstitutionModel will exponentiate any real matrix regardless if the infinitesimal generator contains complex eigenvalues (common in irreversible chains).

21 lines of code changed in 1 file:

• src/dr/math/matrixAlgebra: Matrix.java (+21)

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

25 lines of code changed in 1 file:

• src/dr/math/matrixAlgebra: Matrix.java (+25)

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.

327 lines of code changed in 2 files:

• src/dr/math/matrixAlgebra: Vector.java (+327 -304)

msuchard 2007-12-10 12:46 Rev.: 634

Added generalized GTR model with separate root and stationary distributions for irreversible processes. Added a Dirchlet prior distribution for informative root or stationary distributions. NodeTraitLogger just annotates trees with all traits.

225 lines of code changed in 2 files:

• src/dr/math/matrixAlgebra: LinearEquations.java (new)

msuchard 2007-10-31 04:08 Rev.: 579

Started to add in classes for a multivate OU diffusion process and using Beast for doing (generalized) linear regression problems. May Beast become the new WinBugs!

742 lines of code changed in 2 files:

• src/dr/math/matrixAlgebra: LUPDecomposition.java (+272 -271), Matrix.java (+470 -467)

msuchard 2007-07-08 17:38 Rev.: 367

Added the classes below to implement the multivariate Comparative Method. Unfortunately, MultivariateTraitLikelihood no longer works with the current TreeModel with a HashMap of traitParameters.

MultivariateDiffusionModel
MultivariateTraitLikelihood
MultivariateDistributionLikelihood
InternalTraitGibbsOperator
PrecisionMatrixGibbsOperator
MultivariateDistribution
MultivariateNormalDistribution
WishartDistribution
CorrelationStatistic

313 lines of code changed in 2 files:

• src/dr/math/matrixAlgebra: SymmetricMatrix.java (new)

msuchard 2007-01-13 18:26 Rev.: 127

Removed dependence on numericalMethods.jar. Added Cholesky decomposition class.

63 lines of code changed in 1 file:

• src/dr/math/matrixAlgebra: CholeskyDecomposition.java (new 63)