  We study filtering of multiscale dynamical systems with model error arising
from unresolved smaller scale processes. The analysis assumes continuous-time
noisy observations of all components of the slow variables alone. For a linear
model with Gaussian noise, we prove existence of a unique choice of parameters
in a linear reduced model for the slow variables. The linear theory extends to
to a non-Gaussian, nonlinear test problem, where we assume we know the optimal
stochastic parameterization and the correct observation model. We show that
when the parameterization is inappropriate, parameters chosen for good filter
performance may give poor equilibrium statistical estimates and vice versa.
Given the correct parameterization, it is imperative to estimate the parameters
simultaneously and to account for the nonlinear feedback of the stochastic
parameters into the reduced filter estimates. In numerical experiments on the
two-layer Lorenz-96 model, we find that parameters estimated online, as part of
a filtering procedure, produce accurate filtering and equilibrium statistical
prediction. In contrast, a linear regression based offline method, which fits
the parameters to a given training data set independently from the filter,
yields filter estimates which are worse than the observations or even divergent
when the slow variables are not fully observed.
