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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 $Z_{ir}=1_{\{\text{observation }i\text{ belongs to rat }r\}}$. After integrating out the random intercepts,The fixed-effect design matrix has four independent columns, so the given $A$ has dimensions $176\times 172$, with $A^{T}A=I_{172}$ and $A^{T}X=0$. Consequently the error contrasts $U=A^{T}Y$ have a multivariate normal distribution with mean zero and covariance matrix $W=A^{T}VA$.

The restricted likelihood from orthogonal error contrasts is their density. Equivalently, the estimates maximizeThis is restricted maximum likelihood, not maximization over individual rat effects. The unknown $\beta$ disappears because $A^{T}X=0$. Replacing $A$ by $AQ$ for an orthogonal $Q$ rotates $U$ and conjugates $W$, preserving the determinant and quadratic form; hence the objective is independent of the chosen orthonormal basis. The software's integrated REML log-likelihood can differ by an additive constant depending only on $X$, which has no effect on these variance estimates.