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For a full-rank ordinary least squares design matrix, the hat matrix $H$ and residual projection $G=I-H$ satisfy $HG=GH=0$. Hence fitted values and regression residuals are perpendicular as observed vectors. Under isotropic errors their cross-covariance matrix is zero, and under a normal linear model the two vectors are independent.

Fitted values are the predictions at the predictor values used to fit a regression model. In linear regression with an explicit regression intercept,Here $X$ is the slope design matrix, and $r$ is the regression residual vector. The fitted values estimate the regression function at the observed predictors; they need not equal the observed responses, which may also contain random errors. Prediction at a new predictor vector $x_{\ast }$ uses $\hat{\alpha }+x_{\ast }^T\hat{\beta }$ with the same centering and scaling used in fitting. A prediction interval addresses uncertainty in a new response rather than just displaying this point prediction.

For the five constructed observations in linear regression, ordinary least squares gives fitted values $(4/5,9/5,14/5,19/5,24/5)$. The ridge regression fit at $\lambda =10$ instead gives $(9/5,23/10,14/5,33/10,19/5)$. Both fitted vectors have sample mean $14/5$ because the regression intercept is unpenalized; their regression residuals differ and their residual sums of squares are $4/5$ and $33/10$, respectively.

For ordinary least squares, the fitted values are the orthogonal projection of $Y$ onto the column space of the complete design matrix, including its regression intercept column. They remain unique even in rank-deficient ordinary least squares, although the regression coefficients can be nonunique. The regression residuals are then orthogonal to every column.^[ref] With centered slopes, ridge regression instead satisfies $X_c^{T}r=\lambda {\hat{\beta }}_{\lambda }$, so the regression residuals need not be orthogonal to the slope columns. Their sum is still zero because the regression intercept remains free.

For fixed predictors and scales and a fixed positive penalty, ridge regression gives a linear smoother,For $\lambda >0$ with at least one nonzero slope direction, this matrix is not an orthogonal projection matrix: applying it twice shrinks that direction again. Its effective degrees of freedom are $1+{\sum }_{j=1}^r{d}_j^2/(d_j^2+\lambda )$, where $d_j$ are the positive singular values of $X_c$; the extra $1$ counts the free regression intercept. If the penalty is selected using $Y$, the resulting fitting rule need not be a linear smoother, since its chosen $H_{\lambda }$ also depends on $Y$.

Linear regression models a response's conditional expectation as a linear combination of specified predictors. In matrix form,where the design matrix $X$ describes the observations, $\beta$ contains the regression coefficients, and $\epsilon$ contains the errors. The fitted values $X\hat{\beta }$ estimate the response means. The model is linear in its regression coefficients; its columns may include powers, interactions, or other transformed predictors, so polynomial regression can fit curved relationships using the same machinery.

For a concrete example, take five constructed observationsAn ordinary least squares fit with an intercept gives the line $\hat{y}=0.8+x$. Its regression residuals are $(0.2,0.2,-0.8,0.2,0.2)$ and its residual sum of squares is $0.8$. A one-unit increase in the predictor corresponds to a one-unit increase in the fitted response. This is a description of this fitted association; interpreting a change as a causal effect requires the assumptions of a causal inference problem.

The geometric reason for the fit is simple. The possible mean vectors $X\beta$ form the column space of $X$. Ordinary least squares chooses the orthogonal projection of the data vector onto that vector subspace, so the remaining regression residual is orthogonal to every permitted fitted direction. The least-squares normal equations express this orthogonality as $X^T(Y-X\hat{\beta })=0$. The data's explained component and unexplained component are therefore separated by the same geometry used in a Hilbert space.

The optimization definition makes sense for any observed data. Quantifying the uncertainty of the regression coefficients needs additional assumptions about the sampling and errors. With fixed $X$ of full column rank and mean-zero errors with covariance matrix ${\sigma }^{2}I$, ordinary least squares is unbiased and has covariance ${\sigma }^2(X^{T}X{)}^{-1}$; the Gauss-Markov theorem compares it with other linear unbiased estimators. A normal linear model additionally makes Student t-distribution intervals and tests exact in finite samples. Model adequacy and predictive assessment remain relevant even when these calculations are available.

Two historical settings help explain the subject's appeal. Adrien-Marie Legendre's Nouvelles méthodes pour la détermination des orbites des comètes (1805) includes an appendix on the method of least squares: observations give more equations than unknowns, and squared errors provide a criterion for reconciling them. Its astronomical setting shows the motivation for combining imperfect measurements. ^[ref] Francis Galton's Regression Towards Mediocrity in Hereditary Stature (1886) examines the association between parental and offspring heights and the tendency of group averages toward the population average. This is a historical use of the regression name; the modern linear model is a general statistical formulation. ^[ref]

Minimizing $\Vert y-X\theta {\Vert }^2$ gives the displayed equations by differentiation. Equivalently, the regression residual $r=y-X\hat{\theta }$ satisfies $X^{T}r=0$: it is orthogonal to every column of the design matrix. If $X$ has full column rank, the minimizer is unique and the fitted values are the orthogonal projection of $y$ onto its column space. A rank-deficient design matrix can give multiple coefficient vectors, while the projected fitted vector is still unique.

For an intercept and one predictor, put $S_{xx}={\sum }_i(x_i-\bar{x}{)}^2$ and $S_{xy}={\sum }_i(x_i-\bar{x})(y_i-\bar{y})$. The equations give $\hat{\beta }=S_{xy}/S_{xx}$ and $\hat{\alpha }=\bar{y}-\hat{\beta }\bar{x}$, provided $S_{xx}>0$. In the five-point example in linear regression, $\bar{x}=2$, $\bar{y}=2.8$, $S_{xx}=10$ and $S_{xy}=10$, giving $\hat{\beta }=1$ and $\hat{\alpha }=0.8$.

The normal equations describe the mathematical optimum, but explicitly forming and inverting $X^{T}X$ can amplify numerical problems. A QR decomposition computes the same least-squares solution through orthogonal coordinates; a singular value decomposition also exposes nearly dependent columns. This connects statistical fitting to numerical linear algebra and the choice of a stable algorithm. ^[ref]

The response errors have standard deviations proportional to $|{\mu }_i|$. Thus, when fitted means approximate the true means, increasing absolute fitted values tends to accompany increasing residual spread. A residual-versus-fitted plot shows a fan for positive means, or spread increasing away from zero for means of either sign. Standardization by one common residual standard deviation, even with the usual regression leverage correction, does not remove this systematic heteroscedasticity.

Under independent errors the exact covariance matrix after fitting iswhere $k>0$ is the common proportionality constant. Hence the simple fan description is a diagnostic tendency, not an assertion that each fitted residual has exactly variance $k{\mu }_i^2$.

For positive responses, the intended variance-stabilizing transformation is the natural logarithm. The delta method givesUse $\log Y_i$ for positive data with modest relative error, then refit and check the transformed mean and residual structure. In particular, if the original mean was $X_i^T\beta$, the transformed mean is approximately $\log (X_i^T\beta )-k/2$, not automatically a linear function of the original covariates.

There is a domain qualification in the literal printed model: a nondegenerate normal distribution has negative support. For positive ${\mu }_i$, the probability of $Y_i\le 0$ is $\Phi (-1/\sqrt{k})$, so a real $\log Y_i$ is not defined throughout the stated sampling model. When $k$ is small this is a negligible-tail approximation, not an exact transformation to normal errors. If signed values must be retained and all ${\mu }_i\ne 0$, write $Y_i={\mu }_i(1+\sqrt{k}{Z}_i)$ with standard normal $Z_i$. ThenThe second term has a common distribution with finite variance, so log absolute value stabilization of a normal scale family is exact, but loses the sign of the mean and does not produce normal errors. Zeros and a zero mean are excluded from this transform. Alternatively retain the response scale and fit the stated variance model with weighted least squares weights proportional to $1/{\hat{\mu }}_i^2$ where the means stay away from zero. No arbitrary addition of a constant before taking logarithms exactly solves the given variance relation.

Put $G=I-H$. Since $GX=0$, the regression residual vector is $\hat{\epsilon }=G\epsilon$. A linear transformation of a multivariate normal distribution is again multivariate normal, soThis is a singular multivariate normal distribution supported on $\ker X^T$, with dimension $n-p$. In particular,Consequently regression residuals are neither independent nor identically distributed even under the stated model. Their linear constraints include $X^T\hat{\epsilon }=0$, and, if the design matrix contains an intercept, their sum is zero.

Choose an orthonormal basis of the residual space. The coordinates of $G\epsilon$ in that basis are $n-p$ independent $N(0,{\sigma }^2)$ variables, provingFor $n>p$, $s^2$ is an unbiased estimator of ${\sigma }^2$. Orthogonality of $H$ and $G$ gives zero cross-covariance, so the Gaussian fitted and residual vectors are independent. This explains why an appropriate residual-versus-fitted diagnostic has no systematic mean relationship under the model. If $n=p$, no residual information remains for these diagnostics or the variance estimate.

For $h_{ii}<1$, use standardized regression residuals $r_i={\hat{\epsilon }}_i/[s\sqrt{1-h_{ii}}]$ to account for the different residual variances. The diagonal $h_{ii}$ is the regression leverage; $h_{ii}=1$ makes that residual identically zero and cannot be diagnosed by this standardization. With known $\sigma$, the corresponding individually standardized residual has an exact standard normal distribution. With estimated $s$, the internally studentized residual is not exactly normal or a Student t-distribution, and the residuals remain correlated; a normal reference plot is a diagnostic approximation.

Plot the regression residuals or standardized regression residuals against fitted values and each covariate. A persistent curve suggests a misspecified mean, while a fan-shaped spread suggests heteroscedasticity; a scale-location plot helps separate these. A quantile-quantile plot against normal quantiles checks tails, skewness and possible regression outliers. Plot residuals against observation order or time to look for unexplained serial patterns, recognizing that projection already induces the displayed residual covariances. Inspect regression leverage together with Cook's distance for influential observations. Such patterns motivate revising the model; absence of a visible pattern does not prove all its assumptions.

Expanding the ordinary least squares objective givesFor a nonzero vector $v$, $v^T{X}^{T}Xv=\Vert Xv{\Vert }^2>0$, since the design matrix has matrix rank $p$. The Hessian matrix is therefore positive-definite, and $Q$ is strictly convex. Solving its normal equations gives the unique least-squares estimator:Indeed, expansion about this stationary point and $X^T(Y-X\hat{\beta })=0$ give $Q(\beta )=Q(\hat{\beta })+(\beta -\hat{\beta }{)}^T{X}^{T}X(\beta -\hat{\beta })$, which also proves the global minimum directly.

Define the hat matrix $H=X(X^{T}X{)}^{-1}{X}^T$. It is a symmetric matrix and an idempotent linear map, since $H^T=H$ and $H^2=H$, and its image is the column space of $X$. Thus $H$ is the orthogonal projection onto the fitted mean space. The fitted values are $HY$ and the regression residual vector is $(I-H)Y$. Because $I-H$ is also a symmetric matrix and an idempotent linear map,These minimization and projection identities do not need errors with a normal distribution; the normal linear model becomes relevant to the distributional calculations.

For an $n\times p$ design matrix, distinguish the coefficient vector from the fitted-response vector. The ridge regression objective and its solution areThe gradient is $2(X^{T}X+\lambda I_p)\beta -2X^{T}Y$. For $\lambda >0$, $X^{T}X+\lambda I_p$ is a positive-definite matrix, so this is the unique minimizer even if $X$ is rank deficient. The expression with an additional leading $X$ is instead the $n$-vector of fitted values,This distinction corrects the dimensional mismatch in the printed coefficient-estimator notation.

The quadratic penalty discourages large coefficients, exchanging some bias for lower variance. If $X=UD{V}^T$ is a reduced singular value decomposition, with positive singular values $d_k$, thenThe principal-component shrinkage by ridge regression therefore shrinks directions with small $d_k^2$ most strongly. These are precisely the poorly determined directions created by multicollinearity, where ordinary least-squares coefficients can have large variance or fail to be uniquely determined. A positive penalty stabilizes their inversion and sets coefficients in the null space to zero. It does not make the predictors independent or provide a universal risk improvement for every signal. Because the penalty depends on coefficient units, predictors are ordinarily standardized before choosing $\lambda$ by cross-validation. An unpenalized intercept in ridge regression is handled separately by centering; the displayed objective either has no intercept or applies the penalty to every component included in $\beta$.

The ordinary least squares estimate, which is also the maximum-likelihood estimate in this normal linear model, gives the hat matrixIt is the orthogonal projection onto the column space of $X$, so $P^T=P$, $P^2=P$ and $\mathrm{rank}P=p$. Since $(I-P)X=0$, the vector of regression residuals is $\widehat{ϵ}=(I-P)ϵ$, with multivariate normal distributionFor $i\ne j$, its covariance is $-{\sigma }^2{p}_{ij}$, which is generally nonzero. Therefore the regression residuals are generally dependent, even though the original errors are independent random variables.

Fit the model in R, compute its internally studentized residuals with rstandard(fit), and examine a normal Q-Q plot with qqnorm(rstandard(fit)) and qqline(rstandard(fit)). A plot of these regression residuals against the fitted values helps detect a curved mean pattern or nonconstant variance. Approximate agreement with a straight line in the Q-Q plot, with no systematic residual pattern, supports the assumed error model.

Here $p\ll n$. The average leverage is $\mathrm{tr}P/n=p/n$, and ${\sum }_{ij}{p}_{ij}^2=\mathrm{tr}(P^2)=p$. Thus most diagonal corrections and most off-diagonal dependences are small when only a few directions have been removed from a large sample. Also ${\tilde{\sigma }}^2$ estimates ${\sigma }^2$ accurately when $n-p$ is large. These facts make the visual independent-normal approximation reasonable, though exceptional high-leverage observations still deserve attention.

The approximation is not an exact distributional statement: the distribution of an internally studentized Gaussian residual has ${\hat{\eta }}_i^2/(n-p)\sim \mathrm{Beta}(1/2,(n-p-1)/2)$ when $n-p\ge 2$ and $p_{ii}<1$. In particular these residuals are bounded, rather than exactly distributed according to Student's t-distribution. Formal goodness-of-fit calibration should account for fitting and dependence.

The least-squares estimator minimizes $(Y-Xb{)}^T(Y-Xb)$. Differentiation gives $X^{T}X\hat{\beta }=X^{T}Y$, and the full column rank of $X$ makes $X^{T}X$ positive definite. HenceThe fitted values are $\hat{Y}=X\hat{\beta }=HY$, where the hat matrix is $H=X(X^{T}X{)}^{-1}{X}^T$. The regression residuals are $\hat{\epsilon }=Y-\hat{Y}=(I-H)Y$. Since $H$ is the orthogonal projection matrix onto the column space of $X$, $(I-H)X=0$ andThis is a singular multivariate normal distribution supported on the $(n-p)$-dimensional orthogonal complement of the column space: its components are generally correlated. The equality $\hat{Y}=X\hat{\beta }$ puts the fitted vector in that column space, while $X^T\hat{\epsilon }=0$ expresses fitted-residual orthogonality. No residual component lies in an explanatory direction that could improve the least-squares fit.

For the calibration model, write $R_i$ for a reading and $a_i$ for the known amount. The first fit assumes $R_i=\alpha +\beta a_i+{\epsilon }_i$ with independent $N(0,{\sigma }^2)$ errors. Its residual-versus-fitted plot has systematic changes in group means and an increasing within-group spread. These suggest both a nonlinear mean relationship and heteroscedasticity, rather than the random scatter expected from a satisfactory normal linear model.

The Box–Cox transformation plot is a profile log-likelihood for the power parameter $\lambda$. Its maximum is near $0.94$; the horizontal line gives an approximate 95% likelihood-ratio confidence interval, which excludes the untransformed value $1$. Since affine rescaling of the response does not change the fitted mean space, fitting the raw power $R_i^{0.94}$ is equivalent to using $(R_i^{0.94}-1)/0.94$ with an intercept. The second model isIts residual spread is more even, but observation 17 has a conspicuously negative residual near $-9.95$. This motivates checking for an outlier or recording error. The third fit omits that observation; omission should be justified by that investigation, since choosing exclusions from residuals can affect inference. Some group pattern still remains, so the transformation alone does not certify a perfect model.

At an amount of $3$ nanograms, the third fit predicts the transformed meanSimply applying the inverse power gives ${\hat{m}}^{1/0.94}=118.5187$. The requested expected reading needs bias correction after an inverse transformation, since $\mathbb{E}[g(Z)]\ne g(\mathbb{E}[Z])$ for nonlinear $g$. With $q=1/0.94$ and $s=2.832$, a second-order Taylor expansion givesHere the correction uses the residual variance, rather than the variance of the estimated fitted mean. The power-transformed Gaussian model is an approximation for positive readings; the fitted mean is over 31 residual standard deviations above zero, so the negative tail has negligible effect on this local approximation. The ordinary inverse-transformed prediction is therefore essentially $118.52$ at the displayed precision.

The ordinary least squares estimator is $\hat{\beta }=(X^{T}X{)}^{-1}{X}^{T}Y$. Consequently the fitted values and regression residuals areAn affine transformation of a multivariate normal distribution is again multivariate normal, possibly with a singular covariance matrix. For a random vector with covariance matrix $\Sigma$, its transformed covariance matrix is $A\Sigma A^T$. Since $PX=X$, $P^2=P=P^T$ and $(I-P{)}^2=I-P$, these results giveBoth multivariate normal distributions are supported on their respective projected subspaces. In particular, ${\hat{Y}}_i$ has variance ${\sigma }^2{P}_{ii}$ and $e_i$ has variance ${\sigma }^2(1-P_{ii})$; the regression residuals need not be mutually independent.

Because both vectors are linear transformations of the same multivariate normal response, $(\hat{Y},e)$ is jointly multivariate normal. Its cross-covariance matrix isZero cross-covariance implies independence for jointly multivariate normal vectors, including singular ones. Therefore the fitted values and the entire vector of regression residuals are independent. The fitted-residual orthogonality identity gives the zero covariance; the normal distribution assumption is what upgrades it to independence.

For the normal linear model, the log-likelihood isThe full column rank of the design matrix makes $X^{T}X$ invertible. Differentiating in $\beta$ gives the normal equations $X^{T}X\hat{\beta }=X^{T}Y$. With the minimized residual sum of squares substituted, differentiation in ${\sigma }^2$ givesThese are the maximum-likelihood estimators almost surely; $RSS>0$ almost surely when ${\sigma }^2>0$ and $n>p$. The linear transformation of the multivariate normal distribution yieldsDefine the hat matrix $H=X(X^{T}X{)}^{-1}{X}^T$. The fitted values are $\hat{Y}=HY=X\hat{\beta }$, the regression residuals are $e=Y-\hat{Y}=(I-H)Y$, and $RSS=e^{T}e$. The orthogonal projection $I-H$ has rank $n-p$ and annihilates $X\beta$. By Cochran's theorem,Consequently $E({\hat{\sigma }}^2)=(n-p){\sigma }^2/n$, with bias $-p{\sigma }^2/n$. The unbiased estimator isIts square root, the reported residual standard error, estimates $\sigma$; the assertion of unbiasedness applies to the variance, not generally to its square root.

For the paper-strength analysis, let $h_i$ be the measured percentage and $z_i=h_i-\overline{h}$. Both normal linear models use independent errors of common variance ${\sigma }^2$. Their mean functions are ${\beta }_0+{\beta }_1{z}_i$ for lm1, and ${\beta }_0+{\beta }_1{z}_i+{\beta }_2{z}_i^2$ for lm2, with separately fitted coefficients. The reported residual standard errors are $11.82$ and $4.42$, respectively.

For lm1, the estimated conditional expectation at a new percentage $x$ isThe original data mean $\overline{h}$ must be used for centering the new percentage; its numerical value is not supplied in the excerpt. Because ${\sum }_i{z}_i=0$, the two columns of this design matrix are orthogonal, and $\mathrm{Cov}({\hat{\beta }}_0,{\hat{\beta }}_1)=0$. Hence the coefficient standard errors in the output giveThis estimates uncertainty in the mean. Predicting an individual future batch would additionally require the new-error variance, estimated by $11.82^2$.

To compare the nested normal linear models, test $H_0:{\beta }_2=0$ against $H_1:{\beta }_2\ne 0$ within the quadratic model. The Student t-test statistic isIts two-sided p-value is $1.89\times 10^{-8}$. Equivalently $T^2$ is a partial F-test statistic with null distribution $F_{1,16}$. Reject the linear restriction and prefer lm2 at the 5% level. Its residual spread is much smaller; the increase in the coefficient of determination from $0.3054$ to $0.9085$ supports the same conclusion, although the test is the relevant complexity-adjusted comparison.

For regression diagnostics, inspect regression residuals against fitted means and hardwood percentage for omitted curvature, a scale-location plot for nonconstant variance, and a quantile-quantile plot against the normal distribution for departures from the error assumption. Check unusual observations using regression leverage and Cook's distance, and examine residuals in collection or batch order if dependence is plausible. Independence and a common variance require substantive justification as well as these plots; a small p-value for a polynomial term does not itself check the error model.

The ordinary least squares objective has gradient $2X^{T}X\beta -2X^{T}Y$. The normal equation therefore givesThe Gram matrix $X^{T}X$ is a positive-definite matrix because $X$ has full column rank. More explicitly, for any $b$,since $X^T(Y-X\hat{\beta })=0$. This proves that the displayed solution is the unique global minimum.

The fitted values are $\hat{Y}=X\hat{\beta }=HY$, where the hat matrix isThe inverse of the symmetric matrix $X^{T}X$ is symmetric, so $H^T=H$. Multiplication gives $H^2=X(X^{T}X{)}^{-1}(X^{T}X)(X^{T}X{)}^{-1}{X}^T=H$. Thus $H$ is the orthogonal projection onto the column space of the design matrix.

The regression residual vector is $e=Y-\hat{Y}=GY$ with $G=I_n-H$. Consequently $G^T=G$, $G^2=I_n-2H+H^2=G$, and the residual sum of squares isBy fitted-residual orthogonality, $GH=0$. Using $\mathrm{Cov}(Y)={\sigma }^2{I}_n$, the cross-covariance matrix isBoth vectors are jointly normal, so they are also independent by independence of uncorrelated jointly normal variables. The zero covariance calculation itself only needs the common error variance and lack of error correlations.

For the first wind fit, let $v_i$ be wind velocity and $Y_i$ electrical output. The simple linear regression is $Y_i=\alpha +\beta v_i+{\epsilon }_i$, with independent ${\epsilon }_i\sim N(0,{\sigma }^2)$. It has two fitted mean parameters and $25-2=23$ residual degrees of freedom. The missing analysis of variance entries are therefore velocity degrees of freedom $1$, velocity mean square $8.9296$, and residual degrees of freedom $23$. The residual mean square is $1.2816/23\simeq 0.05572$, and $8.9296/(1.2816/23)\simeq 160.25$, consistent with the printed value after rounding.

Because the model includes a regression intercept, the coefficient of determination is the explained sum of squares divided by the total centered sum of squares:A large coefficient of determination does not rule out a wrong mean function. In the PDF's first residual-versus-fitted plot, residuals are negative at both ends and positive in the middle. This curved pattern agrees with the visibly flattening output-versus-velocity relationship and motivates a polynomial regression with a quadratic term.

The second wind model is $Y_i=\alpha +{\beta }_1{v}_i+{\beta }_2{v}_i^2+{\epsilon }_i$, again with independent common-variance normal errors. Its fitted mean is $-1.155898+0.722936v_i-0.038121v_i^2$. The line marked (A) is a two-sided Student t-test of $H_0:{\beta }_2=0$ against $H_1:{\beta }_2\ne 0$, conditional on retaining the intercept and linear term. Under the null hypothesis,Its two-sided p-value is $6.59\times 10^{-8}$. This is far below $0.05$, so reject a purely linear mean in favour of the quadratic fit. Equivalently, the extra-term nested-model F-test has $F=t^2\simeq 63.15$ and null law $F_{1,22}$.

The third fit is a reciprocal-predictor regression, $Y_i=a+b/v_i+{\epsilon }_i$, with estimated mean $2.9789-6.9345/v_i$. It has two mean parameters rather than the quadratic model's three. Its residual standard error is smaller, $0.09417$ versus $0.1227$, and its coefficient of determination is larger, $0.9800$ versus $0.9676$. The corresponding residual sums of squares are approximately $23(0.09417{)}^2=0.20396$ and $22(0.1227{)}^2=0.33122$. The reciprocal fit is preferable on both these fit measures and parsimony. The two models are not nested, so an ordinary extra-term F-test between them is inappropriate. On the common normal-error likelihood, the difference ${\mathrm{AIC}}_3-{\mathrm{AIC}}_2=25\log (0.20396/0.33122)-2\simeq -14.12$ also favours the third model.

Neither lower residual sum of squares nor a higher coefficient of determination establishes adequate assumptions. The quadratic residual-versus-fitted plot removes the original pronounced curvature; the reciprocal plot also has no comparably obvious mean trend. The low-output residuals appear somewhat more spread out, so check scale-location plots and residuals against velocity for heteroscedasticity. Q-Q plots assess normality; residuals against observation order assess serial dependence; regression leverage and Cook's distance identify influential observations. Further cross-validation, replicate observations at comparable velocities, and prediction errors would help choose between their extrapolation behaviours. Both fitted shapes should be judged principally over the observed positive-velocity range.

Let $\hat{\beta }=(X^{T}X{)}^{-1}{X}^{T}Y$, $H=X(X^{T}X{)}^{-1}{X}^T$, ${\hat{y}}_i=x_i^T\hat{\beta }$, and $e_i=y_i-{\hat{y}}_i$. The horizontal axis of the residual-versus-fitted plot is ${\hat{y}}_i$, the fitted values, and the vertical axis is $e_i$, the regression residual, in millimetres. Under the normal linear model, $\mathrm{Var}(e_i)={\sigma }^2(1-h_{ii})$, where $h_{ii}$ is the regression leverage.

In the quantile-quantile plot, the vertical values are the ordered standardized regression residualsand the horizontal values are corresponding theoretical quantiles ${\Phi }^{-1}(p_k)$ of the standard normal distribution, with plotting positions such as $p_k=(k-1/2)/n$. The exact plotting-position convention has little practical effect here. Under Gaussian errors these points should approximately follow a straight line; they are not independent because fitting induces residual correlations.

The main visible concern is curvature in the conditional mean. The red smooth in the residual-versus-fitted plot descends from positive residuals at low fitted values, becomes negative in the middle, and rises again at high fitted values. This suggests the strictly linear time effects may be inadequate. There is no clear monotone widening of the residual scatter, so strong heteroscedasticity is not apparent. The quantile-quantile plot has modest tail deviations and a few labelled observations, but does not show a dramatic departure from normality. These plots cannot establish independence across days or laboratories; check residuals against day, laboratory, and sampling order as well. A large coefficient of determination does not remove the visible mean-model concern.

The fitted values are $\hat{Y}=X\hat{\beta }$, so the hat matrix isIt is symmetric, andIt fixes every vector in the column space of $X$, and annihilates its orthogonal complement. Thus $H$ is the orthogonal projection onto that column space, has matrix rank and trace $p$, and $I-H$ is the complementary orthogonal projection. ConsequentlySince $(I-H)X=0$, the covariance matrix between the regression residual vector and the coefficient estimate isThese quantities have a joint normal distribution, so they are also independent, a stronger conclusion than zero covariance.

Now $\hat{e}=(I-H)\epsilon$ has mean zero. Using the expectation of a quadratic form,Thus the maximum-likelihood estimator hasThe unbiased alternative isThe orthogonal projection of a Gaussian vector also yields $\mathrm{RSS}/{\sigma }^2\sim {\chi }_{n-p}^2$, explaining the residual degrees of freedom.

The violated assumption is independence of random variables across observations: repeated measurements on the same rat form clustered data. A persistent rat-specific weight difference induces positive within-rat covariance, even after adjustment for time and diet. Treating all 176 measurements as independent is pseudoreplication.

For the claimed lack of identifiability in the second fit, Rat must be a categorical variable, as intended by the rat-effect interpretation. Each rat receives only one diet, so this is confounding of nested fixed factors. If $z_r$ is the rat-indicator column, the diet-$d$ indicator is ${\sum }_{r:D_r=d}{z}_r$. Thus a diet effect can be increased by $c_d$ and every corresponding rat effect decreased by $c_d$, leaving all fitted values unchanged. With an intercept, two diet columns, fifteen rat contrasts and time, there are 19 columns but only 17 independent columns: the intercept and rat contrasts already span the diet columns, while time varies within rats. This gives rank-deficient ordinary least squares.

The first model ignores within-rat dependence; the second cannot separate unrestricted fixed diet and rat effects. If Rat were instead encoded as a single numeric predictor, the asserted rank deficiency would not follow merely from nesting.