BTRY 6940: Inference in Nonlinear Dynamical Systems

Tuesday, Thursday 1:25 - 2:40, Comstock 1187

Slides from opening lecture, and R code for SIR models.

R Code for experiments with a Lotka-Volterra System.

R Code demonstrating some bifurcation systems.

The matcont page for numerical bifurcation analysis.

Some R experiments on bifurcation analysis.

Experiments with Nonlinear Least Squares based on solving ODE's (otherwise called 'trajectory matching').

Papers Jaeger et al on the Gap Gene Network and Colijn and Mackey on Hematopoeisis for discussion.

Papers Word et al on collocation methods with stochastic dynamic systems.

Wood in Nature on fitting models to match features in data.

Ellner on Gradient Matching as a means of estimating parameters.

Beninca et al on chaos in a long-term plankton experiment; also supplementary materials; and an older paper on the challenges of finding chaos

R Code with some gradient matching experiments.

R Code calculating Lyapunov exponents for the Lorenz system.

A couple of papers looking at seasonal effects in Measles. One by He, Ionides and King and one by Word et al.

Stochastic systems biology: a paper by Golightly and Wilkinson.

An example of particle filtering in R code and maximum smoothed log likelihood.