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The calculation is principal component analysis on a correlation matrix, rather than on an unscaled covariance matrix. For each of the eleven rating variables, subtract its column mean and divide by its column standard deviation. If $Z$ is the resulting $43\times 11$ matrix, use the divisor convention of the fitted object to writeHere the scaling standard deviations use divisor $43$, consistently with this convention. Using sample standard deviations with divisor $42$ gives the same correlation matrix and directions, with the corresponding score scale. Every diagonal entry of $R$ is one, so ${\sum }_k{\lambda }_k=\mathrm{tr}R=11$.

A principal component is the linear combination of the standardized ratings along $a_k$. Its principal component score for judge $i$ is $t_{ik}=z_i^T{a}_k$, and its variance is ${\lambda }_k$. The displayed component standard deviations are $\sqrt{{\lambda }_k}$; the explained variance of a principal component is ${\lambda }_k/11$. In particular,The first component explains about $92.122\%$ of the standardized variation, and the first two jointly explain $95.982\%$. Components three, four and five add about $2.321\%$, $0.830\%$ and $0.339\%$. The cumulative line adds these proportions successively; it is not the proportion explained by that component alone. Retaining two components discards about $4.018\%$ of the total standardized squared variation.

The displayed principal component loadings are the unit eigenvector coefficients $a_{jk}$. The first direction has positive, broadly similar weights for all ratings. It measures an overall favorable-rating tendency: a judge high on most ratings has a high first score. The second direction compares integrity and demeanour, with large positive coefficients, against such attributes as decision promptness, case-flow management and physical ability, with negative coefficients. Thus among similarly rated judges, a positive second score indicates relatively stronger integrity/demeanour compared with those operational ratings. This is a description of a data direction, not a causal interpretation. Multiplying a whole eigenvector and its scores by minus one reflects the display but changes nothing substantive.

These principal component loadings are not themselves variable-component correlations. With standardized variables,For example, the integrity correlation with component one is approximately $3.1833\times 0.289\simeq 0.920$. Blank loadings in the printed second column indicate suppressed small entries, not exact zeros. The complete unrounded loading vectors in the fitted object must be used to calculate scores.

A two-dimensional representation plots the 43 pairswith each point labeled by its judge. In the fitted software object these are the first two columns of the score matrix. Nearby points have similar projections of their standardized ratings. The rank-two reconstruction ${\hat{z}}_i=t_{i1}{a}_1+t_{i2}{a}_2$ is the orthogonal projection onto the leading principal plane and minimizes the total squared reconstruction error over all two-dimensional linear subspaces. To see this, for any orthonormal pair of directions the captured variance is the sum of its two Rayleigh quotients, at most ${\lambda }_1+{\lambda }_2$ by diagonalizing $R$; the remaining variance is the total minus that captured sum. Distances in the plot omit the smaller components, so a close projected pair need not be equally close in every original rating. The actual 43 coordinates cannot be recovered from the summary alone; the supplied data matrix or fitted score matrix is needed.

The printed descriptive list omits INTG, although the loading table includes it. INTG denotes integrity and supplies the eleventh variable. The standard data set also contains a contacts variable; the stated eleven-rating analysis uses the ratings, not contacts.

The command centres the log measurements and performs principal component analysis of their covariance matrix. With cor=F, it does not first standardize the variables to variance one. For a unit principal component loading vector $q$, the score $q^T(z_i-\bar{z})$ has sample variance $q^T\hat{\Sigma }q$. By the spectral theorem for real symmetric matrices, expand $q$ in an orthonormal eigenbasis; that variance is a weighted average of the eigenvalues. Its maximum is the largest eigenvalue, reached at the corresponding eigenvector. Repeating subject to orthogonality to previous directions gives the other principal components.

The software uses the divisor-$31$ sample covariance matrix for its component standard deviations, whereas var used divisor $30$. Diagonalizing the displayed matrix gives approximatelyTaking square roots of the latter gives $(0.5671603,0.07312405,0.03064834)$, agreeing with the output to the rounding of the displayed sample covariance matrix. The normalization changes these numerical standard deviations but leaves the eigenvectors and proportions of explained variance of a principal component unchanged.

The first principal component explains about $98.08\%$ of the total log-variable variance, the second another $1.63\%$, and the last about $0.286\%$. Keeping two preserves about $99.714\%$. An original scree plot displays the sharp drop after the first component:

Consequently the centered cloud is very elongated along one direction: a one-dimensional approximation represents almost all of its squared variation. From the displayed covariance matrix, a unit first eigenvector, with its arbitrary sign chosen positive, is approximatelyIts principal component score is therefore $0.3980(\log G_i-\overline{\log G})+0.09514(\log H_i-\overline{\log H})+0.9124(\log V_i-\overline{\log V})$. All coefficients have the same sign, so this direction describes overall tree size, with log volume dominating the unstandardized variation. The summary alone supplies proportions, not the loading directions; the displayed sample covariance matrix supplies the latter. This is a geometric approximation, not evidence of an exact deterministic relation or independent original variables.

One further use is principal component analysis on a correlation matrix, obtained with cor=T, which equalizes marginal variances and answers a different scaling-sensitive question. Another is principal component regression: fit a response to selected principal component scores rather than highly correlated original predictors, choosing the number using prediction assessment. The fitted transformation also projects new measurements into the same low-dimensional coordinates, provided the training centering and scaling are retained.

For the sample, put $\bar{x}=n^{-1}{\sum }_i{x}_i$ and use the sample covariance matrixOrder its eigenvalues ${\hat{\lambda }}_j$ decreasingly and choose unit orthogonal eigenvectors ${\hat{\ell }}_j$. The sample principal components are the score columnsTheir sample means are zero and their sample covariance is diagonal, since ${\hat{\ell }}_j^{T}S{\hat{\ell }}_k={\hat{\lambda }}_j{1}_{\{j=k\}}$. The $j$th sample variance is ${\hat{\lambda }}_j$, and its explained variance of a principal component is ${\hat{\lambda }}_j/\mathrm{tr}(S)$. Using divisor $n$ instead changes the numerical variances by a common factor but leaves the component directions unchanged.

Standardizing means replacing a variable with positive sample variance by $(x_{ij}-{\bar{x}}_j)/s_j$. This gives principal component analysis on a correlation matrix, using $C=D^{-1/2}S{D}^{-1/2}$ with $D=\mathrm{diag}(S)$. It removes arbitrary differences of measurement units and prevents a large-variance coordinate from dominating solely through its scale. It also changes the question being optimized: small-variance and possibly noisy coordinates receive equal marginal weight. Principal component analysis based on the covariance matrix can be more appropriate when the variables have common meaningful units and absolute variability matters. Standardization is therefore a substantive choice, not an automatic improvement. A zero-variance variable must first be removed. In the word-rating example the variables share the same numerical range, but their across-word dispersions can differ; standardization gives each attribute equal initial variance.

For the standardized eight-variable analysis, total variance is $\mathrm{tr}(C)=8$. The first three fractions of explained variance of a principal component are approximately 59.6%, 19.1% and 10.1%, respectively. The first two account for about 78.8%, and the first three for 88.9%. The first direction is dominant but one direction alone loses substantial variation. Retaining two principal components is a plausible descriptive summary: their eigenvalues exceed $1$, whereas the third is below $1$. That cutoff is a heuristic, and the third principal component may still have interpretable content.

The reported coefficient rows are not unit-length vectors. The printed rounded rows have squared lengths $4.7514$, $1.5222$ and $0.8063$, consistent with their eigenvalues to the precision of the coefficient table. They are consistent with the scaled principal component loading convention $r_j=\sqrt{{\lambda }_j}{\ell }_j$. Such rows remain eigenvectors, but the score direction with unit length is ${\ell }_j=r_j/\sqrt{{\lambda }_j}$, or more accurately the row divided by its actual Euclidean norm when using rounded entries. Under this convention $r_{ij}$ is the correlation of standardized attribute $i$ with the variance-one score for component $j$:This explains both their sizes and why they must not be treated as the unit vectors from parts (i) and (ii).

The first principal component has positive coefficients on every attribute, strongest on friendliness, goodness, niceness, bravery and strength. With the favorable endpoints coded in the positive direction, it describes a broad favorable or impressive evaluation, with a potency contribution. The second contrasts movement and speed, with some size and strength, against the first three evaluative attributes; it is chiefly an activity dimension. The third is dominated by size, with smaller positive strength and negative movement/speed coefficients, distinguishing size or potency from activity. These are interpretations of directions of variation, not evidence of causal latent traits. Reversing a principal component's overall sign changes neither its meaning as an axis nor its explained variance; endpoint coding fixes only how its positive side is described.

The first principal component has equal positive coefficients on the three academic subjects and zero coefficient on physical education. It measures overall academic performance in those subjects and explains $71.16\%$ of the variance. The large positive academic covariances explain why these subjects vary predominantly together.

The second principal component has normalized coefficients approximately $(0.099,0,-0.099,0.990)$. It is mainly a physical-education score, with a small adjustment for the physics-versus-mathematics contrast, and explains $12.90\%$ of the variance. The small physical-education covariances with the academic subjects make this direction close to a separate physical-education axis. This is an interpretation of the observed covariance matrix, not proof of distinct causal abilities or statistical independence.

The third principal component compares physics and mathematics together against biology: its coefficient vector is $(1,-2,1,0)/\sqrt{6}$. It captures subject balance rather than overall academic performance, accounting for $9.49\%$ of the variance. The fourth principal component primarily contrasts physics with mathematics, with a smaller physical-education correction; its normalized coefficients are approximately $(0.700,0,-0.700,-0.140)$, and it accounts for the remaining $6.45\%$. Changing all signs in any component reverses its score without changing the interpretation of its contrast or its explained variance of a principal component.

A two-component summary separates broad academic performance from predominantly physical-education performance and retains about $84.06\%$ of the variation. It still discards about $15.94\%$, including differences between academic subjects. Whether that loss is acceptable depends on the purpose: an overall summary may use two principal components, whereas studying subject-specific strengths requires the later principal components too. A single principal component would lose most of the physical-education information.

Let $v_2,v_3,v_4$ be the three supplied coefficient vectors, in their displayed order. Multiplication by the sample covariance matrix givesThe four vectors are pairwise orthogonal, with norms $\sqrt{3}$, $\sqrt{102}$, $\sqrt{6}$ and $\sqrt{204}$. Hence $u_j=v_j/\Vert v_j\Vert$ form an orthonormal basis of eigenvectors. The variance of the principal component with unit coefficient vector $u_j$ is its eigenvalue ${\lambda }_j$. Using unnormalized coefficient vectors would instead give variances ${\lambda }_j\Vert v_j{\Vert }^2$ and would not produce the desired proportions.

The total variance isTherefore the explained variance of a principal component isThe first two principal components together account for $2658/3162\simeq 84.06\%$, and the first three account for $2958/3162\simeq 93.55\%$ of the total variance.

If the change is purely a rescaling of the physics mark, write $X^{\prime }=DX$, where $D=\mathrm{diag}(10/3,1,1,1)$. The sample covariance matrix transforms asThe physics variance is multiplied by $100/9$, becoming approximately $10044.44$. Each covariance between physics and another subject is multiplied by $10/3$, and all other entries stay unchanged. Principal component analysis on this new sample covariance matrix maximizes variance in the new numerical units, so its eigenvectors and explained variance of a principal component generally change. Physics receives disproportionately greater influence simply because its unit has changed.

One solution is to convert the physics marks back to the original scale before doing principal component analysis. Alternatively, use principal component analysis on a correlation matrix: standardize every subject byA positive change of units multiplies both a centered variable and its standard deviation by the same factor. Thus it leaves $Z_j$ and the sample correlation matrix $R$ unchanged.

Correlation-based principal component analysis is invariant under positive changes of units; covariance-based principal component analysis is not. Standardizing gives each subject unit variance, which is a different weighting choice and can emphasize relatively low-variance subjects. If the revised assessment changes the scores themselves rather than just their units, its sample correlation matrix may also change, and mere standardization cannot recover the original analysis.

Principal component analysis replaces correlated measurements by uncorrelated linear compounds ordered by decreasing variance. Keeping the leading compounds gives a low-dimensional summary that preserves as much variance as possible under orthonormal projection. It is an unsupervised description of variation, rather than a guarantee that the high-variance directions are best for classification or prediction.

Write $X_c=X-\mu$. For a unit loading vector $q$, the variance of $q^T{X}_c$ is $q^T\Sigma q$. The spectral theorem gives an orthonormal eigenbasis $q_1,\dots ,q_p$ with eigenvalues ${\lambda }_1\ge \cdots \ge {\lambda }_p\ge 0$. If $q={\sum }_j{b}_j{q}_j$ and ${\sum }_j{b}_j^2=1$, thenEquality is attained at $q_1$. Requiring the next loading to be orthogonal to the first excludes its eigendirection, so the same argument gives $q_2$ and variance ${\lambda }_2$, and continues inductively. Repeated eigenvalues permit any orthonormal basis of the tied eigenspace. These are the population principal components.

With $Q=(q_1,\dots ,q_p)$, set $Y=Q^T{X}_c$. ThenIn particular the components are uncorrelated. They need not be independent unless, for example, $X$ is multivariate normal. FinallyThe trace equality follows from $Q^{T}Q=I$ and cyclicity of trace, so the rotation preserves total variance. The explained variance of a principal component is its eigenvalue divided by this total.

Covariance-based PCA uses centered protein measurements in their original gram units. Its total variance is $218.4$. Correlation-based PCA first divides each centered food measurement by its sample standard deviation, giving nine unit-variance variables and total variance nine. Thus it is principal component analysis on a correlation matrix, not an equivalent rotation of the original unscaled measurements.

The variances of cereals and milk together account for $170.9/218.4\approx 78.3\%$ of the original total. Consequently those variables have considerable influence on covariance-based PCA. Its first component is dominated by a cereal coefficient $-0.86$ opposed to milk $0.42$, broadly a cereal-versus-milk contrast. Its second is dominated by milk $0.83$, with cereals $0.40$ and fish $-0.29$. Its third is chiefly white meat $0.80$ versus fish $-0.52$, with a smaller negative milk term. Component signs may all be reversed without changing the analysis; the important features are relative signs and magnitudes.

After standardization, eggs and starch can contribute as strongly as large-variance foods. The first correlation-based component gives positive weight to meat, eggs, milk and starch, opposed principally to cereals and pulses/nuts; eggs now has coefficient $0.43$ despite its small raw variance. The second emphasizes fish and fruit/vegetables negatively, opposed especially to starch and white meat. The third contrasts white meat and fruit/vegetables with milk, fish and red meat. Thus standardization changes both the emphasis and the directions, rather than just the displayed units of the same components.

The explained variance of a principal component must use the appropriate total:Raw and standardized percentages describe different variance objectives and must not be compared as if one method were always superior.

Standardize when relative patterns across variables, rather than their absolute gram-scale variation, should have equal marginal weight. Correlation-based PCA is also insensitive to changing a variable's measurement unit, which covariance-based PCA is not. Here every food group already has the same units, so differing units do not force standardization. If large fluctuations in actual protein amounts are scientifically important, covariance-based PCA is appropriate. If dietary composition across all food groups is the focus, correlation-based PCA can be more informative. Standardization can nevertheless amplify noise in nearly constant variables; the decision should follow the scientific purpose and measurement reliability.