Section 1. Matrix Algebra. 1) If the eigenvalues of matrix M are {2, 1} a) What is the value of the determinant? 2. 1.5 0.

.5 b) Fill in the missing value in the matrix M = 0.5 sum( eigenvalues)= trace, so 1.5. c) Is the matrix M singular or non-singular? non-singular, non zero determinant. 0.75 0.25 1 d) If M-1 = and Mx = 1 , what is x? 0.25 0.75 -1 M {1,1]= [1,1] e) What is the transpose of a matrix? Rows become columns and columns rows. 2) Section 2 Data exploration and preparation. a) If the sample sizes are large what distribution does the squared Mahalanobis' Distance D2 have? 2 b) I have two vectors A = {1 0 0 0 1 1} B = {1 0 0 1 0 1} calculate the Jaccards distance between A and B. 0.5 c) I have another two vectors C={5 3 2} D={4 2 3} calculate the Manhattan distance between C and D. 3 d) What is "Brush and spin"? Interactive 3-D plots, where the data cloud can be rotated to find a good view point. And where particular points can be selected, highlighted and identified. e) What are the main reasons for transforming or standardising data? The main reasons for using transformations are: to put a variable on a more interpretable, appropriate, scale; to remove size effects; to put variables on similar scales; to make the data conform to the assumptions of the chosen analysis, e.g. multivariate normality, homogeneity of covariance matrices, linearity. Section 3 Principal Component Analysis i) I have done a PCA on a correlation matrix and the eigenvalues are: 2.30 1.39 0.51 0.40 0.19 How many PCs should I keep? How did you decide? 2. Using either Kaiser's crterion (>1) or screeplot. ii) In the same PCA the matrix of eigenvectors was:
PC 1 PC 2 0.36 0.34 0.45 0.48 0.57 PC 3 -0.16 0.81 -0.55 -0.08 0.13 PC 4 -0.77 0.25 0.57 -0.03 -0.1 PC 5 -0.06 -0.15 0.06 -0.72 0.68

DO PH SAL PO4 CHLA

-0.49 -0.39 -0.4 0.5 0.44

For the PCs you decided to keep, which variables should be selected for interpretation? How did you decide? For PC1 (using Mardia's criterion 0.7*0.5=0.35) all of them. For PC2 (0.39) SAL PO4, CHLA. Could use equilibrium contribution 0.45. PC1: PO4, DO; PC2: SAL, PO4, CHLA iii) One observation has the centred and standardised values: DO = 0.1, PH = -0.2, SAL = 1.0, PO4 = 1.0, CHLA = 0. What is its score on PC1? 0.1*-.49-0.2*-0.39+1*-.4-1*0.5+0*0.44 = -0.871 iv) What proportion of the total variance is being excluded from the reduced space plot of PC1 against PC2? (0.51+0.4+0.19)/5 = 22% Section 4 Multidimensional Scaling. i) I have done a PCO and got the following eigenvalues: 131.02 96.58 22.86 6.16 2.92 1.65 0.00 -0.84 -2.59 -12.31 How many observations are in the data set? 10 ii) Using the above eigenvalues how adequate would a reduced space plot based on the first two principal axes? Using Mardia's measures: a2 (absolute values) 82% Using a1 (squared values) 97% iii) Why are the eigenvectors in PCO rescaled by the square root of the eigenvalue? The eigenvectors are normed to 1 so the variance along them is wrong, they must be normed to sqrt(eigenvalue) for the variances to be correct. iv) How can you avoid local minima in non-metric MDS Start using the results from a PCO as starting configuration, and/or multiple random starts. Section 5. Cluster Analysis. i) How does complete linkage clustering measure the distance between clusters? The distance between the two farthest apart points in the two clusters

b)
ii) iii) In cluster analysis what does the Pseudo-t2 statistic measure?` Cluster analysis is used for a number of different purposes. List as many as you can.

i) to find groups for classification; ii) to reduce the number of sampling units in an analysis by using a single representative from each cluster of similar individuals; iii) for data exploration and hypothesis generation; iv) for fitting distribution models and estimating their parameters; v) dissecting a continuous data cloud into relatively homogeneous zones; and many more.

iv) How does the k-means method form clusters? By allocation to the nearest centroid, then evaluate the total within cluster sums of squares (trace(W)), change cluster memberships till trace(W) minimised. Section 6. Multiple Regression i) What is partialling used for? When estimating the relationship between two variables by either regression or correlation, partialling allows the linear relationship of those variables with other variables to be corrected for. It is for removing the linear relationship with nuisance variables before calculating the correlation or regression coefficients. Describe two stepwise methods of variable selection in multiple regression? a) Forward stepwise: Add the variable with the largest (partial) correlation given those variables already in the model. Stop when the next variable to be added is "not significant" using an arbitrary stopping rule usually p=0.5 b) Backwards elimination: Remove the variable with the least "significant" partial regression/correlation coefficient. Stop when the variable to be dropped is "significant" using some arbitrary stopping rule. p=0.05 is common. c) Full Stepwise: Start forward, after each addition do a backwards step to check if any variables have now become superfluous. P for addition and p for rejection often same at 0.15. iii) What are standardised regression coefficients? Regression coefficients when the Xs have been standardised to unit variance. Allows comparison of magnitude of bs between variables of different units. iv) Describe two ways in which the assumptions about the regression model could be violated. a)Non-linearity,b) missing variables not being partialled out Section 7: Constrained Ordination. i) In a Redundancy Analysis the total variance of the Y variables was 180, the total variance of the Y variables is 140, and the eigenvalues from the PCA were {90, 30, 20, 15, 15, 10}: In a reduced space plot based on the first two Redundancy Variates, what would be a good measure of adequacy of the plot? st 1 2 RVs explain 120/180 = 66.6% ii) In a redundancy analysis what is the difference in interpretation between Structure Coefficients and Redundancy Coefficients? Structure coefficients are simple correlation coefficients, Redundancy coefficients are partial coefficients, the influence of one X variable keeping the others constant. iii) When do you use a Canonical Correlation Analysis rather than a Redundancy Analysis? When there is no clear dependent and independent variables, when the two sets of variables are regarded as symmetric, equivalent. iv) Describe two of the problems that can affect your interpretation of the results from a Constrained ordinations Non-linearity, Outliers, Collinearity. Section 8. MANOVA and Canonical Discriminant Analysis i) What null hypothesis is tested by a one-way MANOVA? 1 = 2 =..=g The vectors of population means are equal ii) After a MANOVA where the null hypothesis was rejected, how can we identify which variables are most responsible? ii)

Rank the univariate F statistics, examine the structure coefficients on each of the CVs iii) In an experiment with 4 treatments (including a control), each treatment was applied to 10 different sampling units. From each sampling unit 5 variables were measured. What is the dimensionality of the Canonical Variate space, i.e how many Canonical Variates are there? 3 = Number of groups-1 iv) Which of the MANOVA test statistics is generally the most robust? Pillais trace.