This PR represents a major overhaul of the marginal calculation for all models. In place of the current implementation, the joint density with the likelihood is calculated first. The marginals are then obtained by integrating over this 2-dimensional joint density. Normalisation and integrals are calculated using scipy.integrate functions. This leads to a significantly improved prediction accuracy and a theoretically well-supported computationally procedure. Prior distributions are now enforced in all models.
Other changes:
Hellinger_distances and relative_entropy are no longer calculated point-wise
plot_prob_density is now xarray facet-grid compatible and supports plotting variables onto rows and columns. It has been renamed to .plot.facet_grid.density, in line with the dantro naming scheme
sigma kwarg to plot_prob_density is now smoothing
Performance_analysis config of HarrisWilson has been removed; most synthetic datasets from HarrisWilson have also been removed
Parameters and losses are now stored in a consistent way across models
Changes and improvements to the Harris-Wilson and SIR models: the publications from the PNAS paper are now no longer exactly reproduced, but a better overview of the predicted densities is shown
:warning: Major commit :warning: Breaking change
Overview
This PR represents a major overhaul of the marginal calculation for all models. In place of the current implementation, the joint density with the likelihood is calculated first. The marginals are then obtained by integrating over this 2-dimensional joint density. Normalisation and integrals are calculated using
scipy.integratefunctions. This leads to a significantly improved prediction accuracy and a theoretically well-supported computationally procedure. Prior distributions are now enforced in all models.Other changes:
Hellinger_distancesandrelative_entropyare no longer calculated point-wiseplot_prob_densityis now xarray facet-grid compatible and supports plotting variables onto rows and columns. It has been renamed to.plot.facet_grid.density, in line with the dantro naming schemesigmakwarg toplot_prob_densityis nowsmoothingPerformance_analysisconfig ofHarrisWilsonhas been removed; most synthetic datasets fromHarrisWilsonhave also been removedCan this PR be accepted?