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With known covariance parameters, best linear unbiased prediction minimizes prediction-error variance over linear predictors that are unbiased over both observation errors and random effects, for every fixed-effect value. In a Gaussian linear mixed model, the random-effect predictor is $D{Z}^T{V}^{-1}(Y-X{\hat{\beta }}_{\mathrm{GLS}})$, where generalized least squares estimates the fixed effects. Plugging in covariance estimates gives an empirical predictor; its uncertainty must also account for estimating those covariance parameters. It differs from a best linear unbiased estimator of an unknown fixed coefficient.

Assume the known covariance matrix $\Sigma$ is positive definite. The Gaussian likelihood, up to constants, isIts gradient is $X^T{\Sigma }^{-1}(Y-X\beta )$. The negative Hessian matrix $X^T{\Sigma }^{-1}X$ is positive definite because $X$ has full column rank. Thus the unique maximum-likelihood estimator is the generalized least squares estimatorIt is unbiased, and multiplication of its linear coefficient matrix by $\Sigma$ givesIn fact ${\hat{\beta }}_{\mathrm{GLS}}\sim N_p(\beta ,(X^T{\Sigma }^{-1}X{)}^{-1})$. Equivalently, a whitening transformation premultiplies $Y$ and $X$ by ${\Sigma }^{-1/2}$, after which ordinary least squares applies. There is no extra ${\sigma }^2$ factor when $\Sigma$ is the complete known covariance; such a factor appears if only a shape matrix $\Omega$ is known and $\Sigma ={\sigma }^2\Omega$.

The restricted maximum likelihood procedure estimates covariance parameters from error contrasts that remove the unknown fixed effects. Let $X$ have rank $p$ and choose an $n\times (n-p)$ full-rank matrix $A$ with $A^{T}X=0$. Then $A^{T}Y\sim N(0,A^{T}V(\vartheta )A)$ has a likelihood involving the variance parameters $\vartheta$ but not $\beta$. Maximizing that likelihood is restricted maximum likelihood. An equivalent restricted likelihood from orthogonal error contrasts, up to terms independent of $\vartheta$, iswhereAfter estimating $\vartheta$, use generalized least squares for $\hat{\beta }=(X^T{\hat{V}}^{-1}X{)}^{-1}{X}^T{\hat{V}}^{-1}Y$ and the conditional modes from part (b). In an independent-error normal linear model, this covariance procedure reduces to estimating ${\sigma }^2$ by $\mathrm{RSS}/(n-p)$ instead of $\mathrm{RSS}/n$.

The two models being compared have different fixed-effect spaces, so their error contrasts, dimensions, and restricted likelihoods differ. Their REML values are not likelihoods of the same transformed data and must not be used directly for this fixed-effect likelihood-ratio test. Refit both with ordinary maximum likelihood, integrating out the random effects but retaining the original response vector, and maximize each model's marginal likelihood.

The null hypothesis is ${\beta }_1=0$, leaving the random slope variance free; the alternative permits a nonzero population stirring effect. The supplied test has $2({\ell }_1-{\ell }_0)=7.9588$, one extra fixed coefficient, and approximate ${\chi }_1^2$ p-value $0.004786$. Retain the fixed stirring-rate effect at 5%. A mean-zero random slope cannot substitute for an estimated nonzero population slope. The asymptotic calibration assumes regular nuisance covariance parameters and should be interpreted cautiously with only three furnaces; simulation can provide a better finite-sample calibration.

Let $X$ have columns $1,t$, and let $Z$ have one column per incubator, with entry $t_i$ in the column for observation $i$'s incubator and zeros elsewhere. Integrating the Gaussian random effects givesConsequently its marginal log-likelihood isThe likelihood-ratio test of $H_0:{\tau }^2=0$ against ${\tau }^2>0$ usesFor each covariance, the optimizing coefficients are the generalized least squares estimator $(X^T{V}^{-1}X{)}^{-1}{X}^T{V}^{-1}Y$. Both fits should use the same marginal likelihood convention, for example fitting the alternative with update(fly.model, REML=FALSE) and the null as a Gaussian linear model. The displayed alternative REML criterion alone cannot supply $T$.

The variance component is constrained to be nonnegative, and zero lies on the boundary. Thus the interior-parameter hypothesis of Wilks theorem fails; the usual ${\chi }_1^2$ approximation is inappropriate. A $\frac{1}{2}{\delta }_0+\frac{1}{2}{\chi }_1^2$ limit sometimes applies to a single variance component under additional asymptotic conditions, but four incubators do not give a persuasive large-number-of-groups approximation.

Use a parametric bootstrap under the null: estimate $\beta ,{\sigma }^2$ there; simulate independent Gaussian errors with that fitted variance at exactly the observed times and grouping labels; refit both models by maximum likelihood for each simulated sample; and calculate $T^{\ast }$. The upper-tail proportion, conventionally $(1+\#\{T^{\ast }\ge T\})/(B+1)$, estimates the p-value. Boundary fits with estimated ${\tau }^2=0$ must remain in the simulation distribution. A restricted-likelihood ratio and a correspondingly calibrated bootstrap are another option when the fixed-effect design is identical, but one must not mix ordinary and restricted likelihoods in a single statistic.

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.

The log likelihood, up to constants, isDifferentiation gives the generalized least squares estimatorand maximizing over the scale givesThe divisor $n$ is appropriate for maximum likelihood rather than unbiased estimation.