bjmorgan / kinisi

A Python package for estimating diffusion properties from molecular dynamics simulations.
https://kinisi.readthedocs.io
MIT License
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Changing the approach to variance estimation #10

Closed arm61 closed 2 years ago

arm61 commented 2 years ago

In this PR, I have adapted the approach that is taken to find the variance from covariance matrix and mean. Now instead of using likelihood sampling, we produce a range of random samples from the Gaussian process and apply GLS (in a vectorised fashion) to all of these samples. This has involved the introduction of the rtol parameter, which is associated with the tolerance of the matrix inversion for the construction of the Gaussian process. Additionally, the tests have been updated and the documentation (including methodology) modified to reflect this change.