10.11 Covariates in DFA models

It is standard to add covariates to the analysis so that one removes known important drivers. The DFA with covariates is written:

\[\begin{equation} \begin{gathered} \mathbf{y}_t = \mathbf{Z}\mathbf{x}_t+\mathbf{a}+\mathbf{D}\mathbf{d}_t+\mathbf{v}_t \text{ where } \mathbf{v}_t \sim \text{MVN}(0,\mathbf{R}) \\ \mathbf{x}_t = \mathbf{x}_{t-1}+\mathbf{w}_t \text{ where } \mathbf{w}_t \sim \text{MVN}(0,\mathbf{Q}) \end{gathered} \tag{10.12} \end{equation}\]

where the \(q \times 1\) vector \(\mathbf{d}_t\) contains the covariate(s) at time \(t\), and the \(n \times q\) matrix \(\mathbf{D}\) contains the effect(s) of the covariate(s) on the observations. Using form = "dfa" and covariates=<covariate name(s)>, we can easily add covariates to our DFA, but this means that the covariates are input, not data, and there can be no missing values (see Chapter 6 in the MARSS User Guide for how to include covariates with missing values).