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Packages that use SquareMatrix | |
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Likelihood | Provides classes for calculating the likelihood of a tree given a model and an alignment. |
Maths | Provides maths classes. |
Models | Provides classes for defing a phylogenetic model. |
Uses of SquareMatrix in Likelihood |
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Methods in Likelihood that return SquareMatrix | |
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SquareMatrix |
Probabilities.RateProbabilities.getP(Branch b)
Gets the probability matrix for a single branch |
Uses of SquareMatrix in Maths |
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Methods in Maths that return SquareMatrix | |
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SquareMatrix |
SquareMatrix.add(SquareMatrix o)
Adds a matrix to this one and returns a new matrix as the result |
SquareMatrix |
SquareMatrix.divide(SquareMatrix B)
Divides this matrix by another (this / B) and returns a new matrix as the result |
SquareMatrix |
SquareMatrix.eigValuesDiag()
Calculates the Eigenvalues. |
SquareMatrix |
SquareMatrix.eigVectors()
Calculates the Eigenvectors. |
SquareMatrix |
SquareMatrix.exp()
Calculates e^A where A is the current matrix and returns a new matrix as the result |
SquareMatrix |
SquareMatrix.expMult(double x)
Calculates e^Ax where A is this matrix and returns a new matrix as the result. |
SquareMatrix |
EigenvalueDecomposition.getD()
Return the block diagonal eigenvalue matrix |
SquareMatrix |
LUDecomposition.getL()
Return lower triangular factor |
SquareMatrix |
LUDecomposition.getU()
Return upper triangular factor |
SquareMatrix |
EigenvalueDecomposition.getV()
Return the eigenvector matrix |
SquareMatrix |
SquareMatrix.inverse()
Calculates the inverse of this matrix and returns a new matrix as the result. |
SquareMatrix |
SquareMatrix.multiply(SquareMatrix o)
Multiplies this matrix by another (this × o) and returns a new matrix as a result |
SquareMatrix |
SquareMatrix.scalarDivide(double n)
Divides the matrix by a scalar and returns a new matrix as the result |
SquareMatrix |
SquareMatrix.scalarMultiply(double n)
Multiplies the matrix by a scalar and returns a new matrix as the result |
SquareMatrix |
LUDecomposition.solve(SquareMatrix B)
Solve A*X = B |
SquareMatrix |
SquareMatrix.square()
Sqaures the matrix and returns a new Matrix that is the result |
SquareMatrix |
SquareMatrix.transpose()
Transposes the matrix and returns a new matrix as the result |
Methods in Maths with parameters of type SquareMatrix | |
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SquareMatrix |
SquareMatrix.add(SquareMatrix o)
Adds a matrix to this one and returns a new matrix as the result |
SquareMatrix |
SquareMatrix.divide(SquareMatrix B)
Divides this matrix by another (this / B) and returns a new matrix as the result |
SquareMatrix |
SquareMatrix.multiply(SquareMatrix o)
Multiplies this matrix by another (this × o) and returns a new matrix as a result |
SquareMatrix |
LUDecomposition.solve(SquareMatrix B)
Solve A*X = B |
Constructors in Maths with parameters of type SquareMatrix | |
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EigenvalueDecomposition(SquareMatrix Arg)
Check for symmetry, then construct the eigenvalue decomposition |
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LUDecomposition(SquareMatrix A)
LU Decomposition |
Uses of SquareMatrix in Models |
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Methods in Models that return SquareMatrix | |
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SquareMatrix |
RateCategory.getP(double length)
Gets the P-matrix for a given length |
Methods in Models with parameters of type SquareMatrix | |
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static double[] |
Distributions.quasiStationary(SquareMatrix m)
Calculates a quasi-stationary distribution from a given rate matrix. |
static double[] |
Distributions.stationary(SquareMatrix m)
Calculates a stationary distribution from a given rate matrix. |
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