 Solution

Let $X$ have rows $(1,y_i)$ and let ${\Sigma }_{\vartheta }$ be the spatial covariance matrix with $\vartheta =({\tau }^2,{\sigma }^2,a)$. Conditional on chosen covariance parameters, the best linear unbiased estimator of the drift coefficients is the generalized least squares estimatorThe printed procedure first estimates the linear drift from depth ~ y, constructs a binned residual empirical semivariogram, fits a Gaussian semivariogram to it, and then uses the fitted covariance in generalized least squares trend estimation and universal kriging. The missing fit could be supplied aswhere those arguments are initial values, not the reported final estimates. Such semivariogram fitting typically minimizes a weighted sum of squared discrepancies between binned empirical values and model values; it is not automatically a joint Gaussian likelihood maximization. One can iterate: form residuals using the current drift, refit the covariance model, recompute the generalized least squares drift, and repeat until changes are small. The displayed commands themselves show a single sequence, not evidence that such iteration occurred.

A likelihood-based alternative estimates the two blocks coherently fromSubstitute $\hat{\beta }(\vartheta )$ to obtain a profile log-likelihood, maximize over ${\tau }^2,{\sigma }^2\ge 0$ and $a>0$ with a positive-definite matrix ${\Sigma }_{\vartheta }$, and recover the drift coefficients from the optimizing covariance. Restricted maximum likelihood adds the design determinant term $\log \det (X^T{\Sigma }_{\vartheta }^{-1}X)$ and uses $n-2$ in place of $n$ in the normalizing term, up to a fixed-design constant. It can reduce bias from estimating the drift before the covariance. A zero fitted nugget is a legitimate boundary estimate, not proof that measurement error is absent. Estimate drift using covariance-weighted regression, and spatial dependence from drift-adjusted variation, with the two stages or likelihood explicitly distinguished.