./run.sh
This samples from the prior and posterior distributions. The oct/
directory
contains a few functions for plotting these results (GNU Octave and OctBi
required).
A synthetic data set is provided, but a new one one may be generated with
init.sh
(GNU Octave and OctBi required).
This package is based on a Lotka-Volterra model of the interaction between
phytoplankton
The process model is given by the equations:
\begin{eqnarray}
\frac{dP}{dt} &=& \alpha_t P - cPZ \\
\frac{dZ}{dt} &=& ecPZ - m_lZ - m_q Z^2,
\end{eqnarray}
where
This version of the model was originally used in Jones, Parslow & Murray (2010). Its behaviour under sampling with the particle marginal Metropolis-Hastings (PMMH) sampler is also studied in Murray, Jones & Parslow (2013).
Jones, E.; Parslow, J. & Murray, L. M. A Bayesian approach to state and parameter estimation in a Phytoplankton-Zooplankton model. Australian Meteorological and Oceanographic Journal, 2010, 59, 7-16.
Murray, L. M.; Jones, E. M. & Parslow, J. On collapsed state-space models and the particle marginal Metropolis-Hastings sampler, 2013.