Nonparametric Bayes

Continuing sensitivity analysis

The commit log to and earlier to (now depricated) capture the summary figures for replicate runs of the observation data, with commits corresponding to various parameter configurations, etc. Here is a nice collection of replicates from

  • Harvest during observations Tweaked calculation of observation data given the harvest regime under which observations were taken (simulation was not implementing all harvests).

  • Also adjusted norm used in GP (the parametric use log-normal densities in calculating the transition function on the untransformed data. The GP, also on untransformed data, uses normal noise as per its model).

  • Relaxed priors, shows no impact on GP performance.

Non-stationary dynamics

  • Ran the Allen et al. Allee model under conditions for non-stationary stable states (e.g. period 2, period 4) etc, with and without substantial process noise (to confirm the cyclical pattern). Shows good performance of GP against terrible perfomance of alternative parametric approaches. Closes issue #16
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Commit log links to some additional examples:

  • another allee example altering MLE initial condition to attempt better likelihood estimates. GP still outperforms. 04:40 pm 2012/12/27
  • in oscillatory regime with non-negligible noise. again GP performs nearly optimally while MLE methods suffer greatly 04:27 pm 2012/12/27
  • Example of Ricker-Allee in oscillation regime, shows non-trivial dynamics, GP does very well (closes #22) 04:17 pm 2012/12/27
  • work with non-named arguments in MLE, consistent ordering for plot legends 04:05 pm 2012/12/27

Other projects

  • Upgraded gems, had to update notebook’s liquid code metadata to handle dates in string format on pages vs being date objects in posts. de4d4cc

  • Setting up multiple_uncertainty as a separate repository (branched from pdg-control).