I require that the cholesky return an upper triangular matrix,
but did not explain this in the text.
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"\\Sigma = \\mathbf{SS}^\\mathsf T\n",
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"$$\n",
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"\n",
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"This definition is favored because $\\mathbf S$ is computed using the [*Cholesky decomposition*](https://en.wikipedia.org/wiki/Cholesky_decomposition) [3]. It decomposes a Hermitian, positive-definite matrix into a lower triangular matrix and its conjugate transpose. $\\mathbf P$ has these properties, so we can treat $\\mathbf S = \\text{cholesky}(\\mathbf P)$ as the square root of $\\mathbf P$.\n",
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"This definition is favored because $\\mathbf S$ is computed using the [*Cholesky decomposition*](https://en.wikipedia.org/wiki/Cholesky_decomposition) [3]. It decomposes a Hermitian, positive-definite matrix into a triangular matrix and its conjugate transpose. The matrix can be either upper \n",
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"or lower triangular, like so:\n",
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"\n",
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"SciPy provides `cholesky()` method in `scipy.linalg`. If your language of choice is Fortran, C, or C++, libraries such as LAPACK provide this routine. Matlab provides `chol()`."
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"$$A=LL^∗ \\\\ A=U^∗U$$\n",
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"\n",
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"The asterick denotes the conjugate transpose; we have only real numbers so for us we can write:\n",
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"\n",
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"$$A=LL^\\mathsf T \\\\ A=U^\\mathsf T U$$\n",
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"\n",
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"$\\mathbf P$ has these properties, so we can treat $\\mathbf S = \\text{cholesky}(\\mathbf P)$ as the square root of $\\mathbf P$.\n",
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"\n",
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"SciPy provides `cholesky()` method in `scipy.linalg`. If your language of choice is Fortran, C, or C++, libraries such as LAPACK provide this routine. Matlab provides `chol()`.\n",
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"\n",
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"By default `scipy.linalg.cholesky()` returns a upper triangular matrix, so I elected to write the code to expect an upper triangular matrix. If you provide your own square root implementation you will need to take this into account."
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]
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},
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{
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