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NAGJavaExamples

Examples demonstrating the nAG Library for Java

Important Information

This file has a lot of Latex and GitHub currently cannot render it on Markdown files. You can read all the math clearly as a webpage or access this as a regular github repository.

The source of this example can be found here and the output here.

See the top directory of this repository for instructions to set up the NAG Library for Java.

Nearest Correlation Matrices

This notebook looks at computing nearest correlation matrices using the NAG Library for Java.

Correlation Matrices

Empirical Correlation Matrices

Computing Correlation Matrices

\[\large S_{ij}=\frac{1}{m-1}(p_i - \bar{p}_i )^T(p_j - \bar{p}_j)\] \[\begin{align*} \large D_S^{1/2} & = \large \textrm{ diag}(s_{11}^{-1/2},s_{22}^{-1/2}, \ldots, s_{nn}^{-1/2}) \nonumber \\ & \\ \large R & = \large D_S^{1/2} S D_S^{1/2} \end{align*}\]

Approximate Correlation Matrices

Missing Stock Price Example

  Stock A Stock B Stock C Stock D Stock E Stock F Stock G Stock H
Month 1 59.875 42.734 47.938 60.359 54.016 69.625 61.500 62.125
Month 2 53.188 49.000 39.500   34.750   83.000 44.500
Month 3 55.750 50.000 38.938   30.188   70.875 29.938
Month 4 65.500 51.063 45.563 69.313 48.250 62.375 85.250  
Month 5 69.938 47.000 52.313 71.016   59.359 61.188 48.219
Month 6 61.500 44.188 53.438 57.000 35.313 55.813 51.500 62.188
Month 7 59.230 48.210 62.190 61.390 54.310 70.170 61.750 91.080
Month 8 61.230 48.700 60.300 68.580 61.250 70.340    
Month 9 52.900 52.690 54.230   68.170 70.600 57.870 88.640
Month 10 57.370 59.040 59.870 62.090 61.620 66.470 65.370 85.840
\[P=\left[\begin{array}{rrrrrrrr} 59.875 & 42.734 & {\color{blue}{47.938}} & {\color{blue}{60.359}} & 54.016 & 69.625 & 61.500 & 62.125 \\ 53.188 & 49.000 & 39.500 & \textrm{NaN} & 34.750 & \textrm{NaN} & 83.000 & 44.500 \\ 55.750 & 50.000 & 38.938 & \textrm{NaN} & 30.188 & \textrm{NaN} & 70.875 & 29.938 \\ 65.500 & 51.063 & {\color{blue}{45.563}} & {\color{blue}{69.313}} & 48.250 & 62.375 & 85.250 & \textrm{NaN} \\ 69.938 & 47.000 & {\color{blue}{52.313}} & {\color{blue}{71.016}} & \textrm{NaN} & 59.359 & 61.188 & 48.219 \\ 61.500 & 44.188 & {\color{blue}{53.438}} & {\color{blue}{57.000}} & 35.313 & 55.813 & 51.500 & 62.188 \\ 59.230 & 48.210 & {\color{blue}{62.190}} & {\color{blue}{61.390}} & 54.310 & 70.170 & 61.750 & 91.080 \\ 61.230 & 48.700 & {\color{blue}{60.300}} & {\color{blue}{68.580}} & 61.250 & 70.340 & \textrm{NaN} & \textrm{NaN} \\ 52.900 & 52.690 & 54.230 & \textrm{NaN} & 68.170 & 70.600 & 57.870 & 88.640 \\ 57.370 & 59.040 & {\color{blue}{59.870}} & {\color{blue}{62.090}} & 61.620 & 66.470 & 65.370 & 85.840 \end{array}\right].\] \[\begin{align*} \large v_1^T & = \large [47.938, 45.563, 52.313, 53.438, 62.190, 60.300, 59.870] \\ \large v_2^T & = \large [60.359, 69.313, 71.016, 57.000, 61.390, 68.580, 62.090] \\ S_{3,4} & = \large \frac{1}{6} (v_1 - \bar{v}_1 )^T(v_2 - \bar{v}_2) \end{align*}\]

Initialize our P matrix of observations

// Define a 2-d array and use Double.NaN to set elements as NaNs
double[][] P = new double[][] {
        { 59.875, 42.734, 47.938, 60.359, 54.016, 69.625, 61.500, 62.125 },
        { 53.188, 49.000, 39.500, Double.NaN, 34.750, Double.NaN, 83.000, 44.500 },
        { 55.750, 50.000, 38.938, Double.NaN, 30.188, Double.NaN, 70.875, 29.938 },
        { 65.500, 51.063, 45.563, 69.313, 48.250, 62.375, 85.250, Double.NaN },
        { 69.938, 47.000, 52.313, 71.016, Double.NaN, 59.359, 61.188, 48.219 },
        { 61.500, 44.188, 53.438, 57.000, 35.313, 55.813, 51.500, 62.188 },
        { 59.230, 48.210, 62.190, 61.390, 54.310, 70.170, 61.750, 91.080 },
        { 61.230, 48.700, 60.300, 68.580, 61.250, 70.340, Double.NaN, Double.NaN },
        { 52.900, 52.690, 54.230, Double.NaN, 68.170, 70.600, 57.870, 88.640 },
        { 57.370, 59.040, 59.870, 62.090, 61.620, 66.470, 65.370, 85.840 } };

Compute the covariance, ignoring missing values

public static double[][] cov_bar(double[][] P) {
    double[] xi, xj;
    boolean[] xib, xjb, notp;
    int n = P[0].length;
    double[][] S = new double[n][n];
    int notpFalseCount;
    
    for (int i = 0; i < n; i++) {
        // Take the ith column
        xi = getMatrixColumn(P, i);
        
        for (int j = 0; j < i + 1; j++) {
            // Take the jth column, where j <= i
            xj = getMatrixColumn(P, j);
            
            // Set mask such that all NaNs are true
            xib = getNanMask(xi);
            xjb = getNanMask(xj);
            
            notp = addBoolArrOr(xib, xjb);
            
            // S[i][j] = (xi - mean(xi)) * (xj - mean(xj))
            S[i][j] = matrixMaskedDot(vectorSubScalar(xi, vectorMaskedMean(xi, notp)),
                    vectorSubScalar(xj, vectorMaskedMean(xj, notp)), notp);
            
            // Take the sum over !notp to normalize
            notpFalseCount = 0;
            for (boolean b : notp) {
                if (!b) {
                    notpFalseCount++;
                }
            }
            S[i][j] = 1.0 / (notpFalseCount - 1) * S[i][j];
            S[j][i] = S[i][j];
        }
    }
    return S;
}


public static double[][] cor_bar(double[][] P) {
    double[][] S, D;
    S = cov_bar(P);
    // D = 1.0 / SQRT(S)
    D = getMatrixFromDiag(vectorRightDiv(vectorSqrt(getMatrixDiag(S)), 1.0));

    // S_ = S * D
    F01CK f01ck = new F01CK();
    double[] S_ = new double[S.length * S[0].length];
    double[] S1d = convert2DTo1D(S);
    double[] D1d = convert2DTo1D(D);
    int n = S.length;
    int p = n;
    int m = n;
    double[] z = new double[0];
    int iz = 0;
    int opt = 1;
    int ifail = 0;
    f01ck.eval(S_, S1d, D1d, n, p, m, z, iz, opt, ifail);
    
    // D_ = D * S_
    double[] D_ = new double[n * n];
    f01ck.eval(D_, D1d, S_, n, p, m, z, iz, opt, ifail);
    
    return convert1DTo2D(D_, n);
}

Compute the approximate correlation matrix

double[][] G = cor_bar(P);


The approximate correlation matrix
  1.0000  -0.3250   0.1881   0.5760   0.0064  -0.6111  -0.0724  -0.1589 
 -0.3250   1.0000   0.2048   0.2436   0.4058   0.2730   0.2869   0.4241 
  0.1881   0.2048   1.0000  -0.1325   0.7658   0.2765  -0.6172   0.9006 
  0.5760   0.2436  -0.1325   1.0000   0.3041   0.0126   0.6452  -0.3210 
  0.0064   0.4058   0.7658   0.3041   1.0000   0.6652  -0.3293   0.9939 
 -0.6111   0.2730   0.2765   0.0126   0.6652   1.0000   0.0492   0.5964 
 -0.0724   0.2869  -0.6172   0.6452  -0.3293   0.0492   1.0000  -0.3983 
 -0.1589   0.4241   0.9006  -0.3210   0.9939   0.5964  -0.3983   1.0000 

Compute the eigenvalues of our (indefinite) G.

F08NA f08na = new F08NA();
String jobvl = "N";
String jobvr = "N";
int n = G[0].length;
double[] G1d = convert2DTo1D(G);
int lda = G.length;
double[] wr = new double[n];
double[] wi = new double[n];
int ldvl = 1;
double[] vl = new double[ldvl];
int ldvr = 1;
double[] vr = new double[ldvr];
int lwork = 3 * n;
double[] work = new double[lwork];
int info = 0;
f08na.eval(jobvl, jobvr, n, G1d, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
Arrays.sort(wr);


Sorted eigenvalues of G:  -0.2498  -0.0160   0.0895   0.2192   0.7072   1.7534   1.9611   3.5355 

Nearest Correlation Matrices

\[\large \min \frac{1}{2} \| G-X \|^2_F = \min \frac{1}{2} \sum_{i=1}^{n} \sum_{i=1}^{n} \left| G(i,j)-X(i,j) \right| ^2\]

Using G02AA to compute the nearest correlation matrix in the Frobenius norm

// Call NAG routine G02AA and print the result
G02AA g02aa = new G02AA();
G1d = convert2DTo1D(G);
n = G.length;
int ldg = n;
int ldx = n;
double errtol = 0.0;
int maxits = 0;
int maxit = 0;
double[] X1d = new double[ldx * n];
int iter = 0;
int feval = 0;
double nrmgrd = 0.0;
int ifail = 0;
g02aa.eval(G1d, ldg, n, errtol, maxits, maxit, X1d, ldx, iter, feval, nrmgrd, ifail);

double[][] X = convert1DTo2D(X1d, ldx);
iter = g02aa.getITER();


Nearest correlation matrix
  1.0000  -0.3112   0.1889   0.5396   0.0268  -0.5925  -0.0621  -0.1921 
 -0.3112   1.0000   0.2050   0.2265   0.4148   0.2822   0.2915   0.4088 
  0.1889   0.2050   1.0000  -0.1468   0.7880   0.2727  -0.6085   0.8802 
  0.5396   0.2265  -0.1468   1.0000   0.2137   0.0015   0.6069  -0.2208 
  0.0268   0.4148   0.7880   0.2137   1.0000   0.6580  -0.2812   0.8762 
 -0.5925   0.2822   0.2727   0.0015   0.6580   1.0000   0.0479   0.5932 
 -0.0621   0.2915  -0.6085   0.6069  -0.2812   0.0479   1.0000  -0.4470 
 -0.1921   0.4088   0.8802  -0.2208   0.8762   0.5932  -0.4470   1.0000 


jobvl = "N";
jobvr = "N";
n = X[0].length;
lda = X.length;
wr = new double[n];
wi = new double[n];
ldvl = 1;
vl = new double[ldvl];
ldvr = 1;
vr = new double[ldvr];
lwork = 3 * n;
work = new double[lwork];
info = 0;
f08na.eval(jobvl, jobvr, n, X1d, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
Arrays.sort(wr);


Sorted eigenvalues of X:  -0.0000   0.0000   0.0380   0.1731   0.6894   1.7117   1.9217   3.4661 

Weighting rows and columns of elements

\[P=\left[\begin{array}{rrrrrrrr} {\color{blue}{59.875}} & {\color{blue}{42.734}} & {\color{blue}{47.938}} & 60.359 & 54.016 & 69.625 & 61.500 & 62.125 \\ {\color{blue}{53.188}} & {\color{blue}{49.000}} & {\color{blue}{39.500}} & \textrm{NaN} & 34.750 & \textrm{NaN} & 83.000 & 44.500 \\ {\color{blue}{55.750}} & {\color{blue}{50.000}} & {\color{blue}{38.938}} & \textrm{NaN} & 30.188 & \textrm{NaN} & 70.875 & 29.938 \\ {\color{blue}{65.500}} & {\color{blue}{51.063}} & {\color{blue}{45.563}} & 69.313 & 48.250 & 62.375 & 85.250 & \textrm{NaN} \\ {\color{blue}{69.938}} & {\color{blue}{47.000}} & {\color{blue}{52.313}} & 71.016 & \textrm{NaN} & 59.359 & 61.188 & 48.219 \\ {\color{blue}{61.500}} & {\color{blue}{44.188}} & {\color{blue}{53.438}} & 57.000 & 35.313 & 55.813 & 51.500 & 62.188 \\ {\color{blue}{59.230}} & {\color{blue}{48.210}} & {\color{blue}{62.190}} & 61.390 & 54.310 & 70.170 & 61.750 & 91.080 \\ {\color{blue}{61.230}} & {\color{blue}{48.700}} & {\color{blue}{60.300}} & 68.580 & 61.250 & 70.340 & \textrm{NaN} & \textrm{NaN} \\ {\color{blue}{52.900}} & {\color{blue}{52.690}} & {\color{blue}{54.230}} & \textrm{NaN} & 68.170 & 70.600 & 57.870 & 88.640 \\ {\color{blue}{57.370}} & {\color{blue}{59.040}} & {\color{blue}{59.870}} & 62.090 & 61.620 &66.470 & 65.370 & 85.840 \end{array}\right].\] \[\Large \|W^{\frac{1}{2}} (G-X) W^{\frac{1}{2}} \|_F\]

Use G02AB to compute the nearest correlation matrix with row and column weighting

// Define an arrray of weights
double[] W = new double[] { 10, 10, 10, 1, 1, 1, 1, 1 };

// Set up and call the NAG routine using weights and a minimum eigenvalue
G02AB g02ab = new G02AB();
G1d = convert2DTo1D(G);
ldg = G.length;
n = G[0].length;
String opt = "B";
double alpha = 0.001;
errtol = 0.0;
maxits = 0;
maxit = 0;
ldx = n;
X1d = new double[ldx * n];
iter = 0;
feval = 0;
nrmgrd = 0;
ifail = 0;
g02ab.eval(G1d, ldg, n, opt, alpha, W, errtol, maxits, maxit, X1d, ldx, iter, feval, nrmgrd, ifail);

X = convert1DTo2D(X1d, ldx);
iter = g02ab.getITER();


Nearest correlation matrix using row and column weighting
  1.0000  -0.3250   0.1881   0.5739   0.0067  -0.6097  -0.0722  -0.1598 
 -0.3250   1.0000   0.2048   0.2426   0.4060   0.2737   0.2870   0.4236 
  0.1881   0.2048   1.0000  -0.1322   0.7661   0.2759  -0.6171   0.9004 
  0.5739   0.2426  -0.1322   1.0000   0.2085  -0.0890   0.5954  -0.1805 
  0.0067   0.4060   0.7661   0.2085   1.0000   0.6556  -0.2780   0.8757 
 -0.6097   0.2737   0.2759  -0.0890   0.6556   1.0000   0.0490   0.5746 
 -0.0722   0.2870  -0.6171   0.5954  -0.2780   0.0490   1.0000  -0.4550 
 -0.1598   0.4236   0.9004  -0.1805   0.8757   0.5746  -0.4550   1.0000 


jobvl = "N";
jobvr = "N";
n = X[0].length;
lda = X.length;
wr = new double[n];
wi = new double[n];
ldvl = 1;
vl = new double[ldvl];
ldvr = 1;
vr = new double[ldvr];
lwork = 3 * n;
work = new double[lwork];
info = 0;
f08na.eval(jobvl, jobvr, n, X1d, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
Arrays.sort(wr);


Sorted eigenvalues of X:   0.0010   0.0010   0.0305   0.1646   0.6764   1.7716   1.8910   3.4639 


Weighting Individual Elements

\[\Large \|H \circ(G-X) \|_F\]

Use G02AJ to compute the nearest correlation matrix with element-wise weighting

// Set up a matrix of weights
n = P[0].length;
double[][] H = new double[n][n];
for (int i = 0; i < n; i++) {
    for (int j = 0; j < n; j++) {
        if ((i < 3) && (j < 3)) {
            H[i][j] = 100.0;
        } else {
            H[i][j] = 1;
        }
    }
}


100.0000 100.0000 100.0000   1.0000   1.0000   1.0000   1.0000   1.0000 
100.0000 100.0000 100.0000   1.0000   1.0000   1.0000   1.0000   1.0000 
100.0000 100.0000 100.0000   1.0000   1.0000   1.0000   1.0000   1.0000 
  1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000 
  1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000 
  1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000 
  1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000 
  1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000   1.0000 


// Call the NAG routine specifying a minimum eigenvalue
G02AJ g02aj = new G02AJ();
G1d = convert2DTo1D(G);
ldg = G.length;
n = G[0].length;
alpha = 0.001;
double[] H1d = convert2DTo1D(H);
int ldh = H.length;
errtol = 0;
maxit = 0;
ldx = n;
X1d = new double[ldx * n];
iter = 0;
double norm2 = 0;
ifail = 0;
g02aj.eval(G1d, ldg, n, alpha, H1d, ldh, errtol, maxit, X1d, ldx, iter, norm2, ifail);

X = convert1DTo2D(X1d, ldx);
iter = g02aj.getITER();


Nearest correlation matrix using element-wise weighting
  1.0000  -0.3251   0.1881   0.5371   0.0255  -0.5893  -0.0625  -0.1929 
 -0.3251   1.0000   0.2048   0.2249   0.4144   0.2841   0.2914   0.4081 
  0.1881   0.2048   1.0000  -0.1462   0.7883   0.2718  -0.6084   0.8804 
  0.5371   0.2249  -0.1462   1.0000   0.2138  -0.0002   0.6070  -0.2199 
  0.0255   0.4144   0.7883   0.2138   1.0000   0.6566  -0.2807   0.8756 
 -0.5893   0.2841   0.2718  -0.0002   0.6566   1.0000   0.0474   0.5930 
 -0.0625   0.2914  -0.6084   0.6070  -0.2807   0.0474   1.0000  -0.4471 
 -0.1929   0.4081   0.8804  -0.2199   0.8756   0.5930  -0.4471   1.0000 


jobvl = "N";
jobvr = "N";
n = X[0].length;
lda = X.length;
wr = new double[n];
wi = new double[n];
ldvl = 1;
vl = new double[ldvl];
ldvr = 1;
vr = new double[ldvr];
lwork = 3 * n;
work = new double[lwork];
info = 0;
f08na.eval(jobvl, jobvr, n, X1d, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
Arrays.sort(wr);


Sorted eigenvalues of X:   0.0010   0.0010   0.0375   0.1734   0.6882   1.7106   1.9224   3.4660 


Fixing a Block of Elements

\[\large X = \alpha \left( \begin{array}{ll}G_{11} & 0 \\ 0 & I \end{array} \right) +(1-\alpha)G, \qquad G = \left( \begin{array}{ll} G_{11} & G_{12} \\ G_{12}^T & G_{22} \end{array} \right)\]

Use G02AN to compute the nearest correlation matrix with fixed leading block

// Call the NAG routine fixing the top 3-by-3 block
G02AN g02an = new G02AN();
G1d = convert2DTo1D(G);
ldg = G.length;
n = G[0].length;
int k = 3;
errtol = 0;
double eigtol = 0;
ldx = n;
X1d = new double[ldx * n];
alpha = 0.001;
iter = 0;
double eigmin = 0;
norm2 = 0;
ifail = 0; 
g02an.eval(G1d, ldg, n, k, errtol, eigtol, X1d, ldx, alpha, iter, eigmin, norm2, ifail);

X = convert1DTo2D(X1d, ldx);
iter = g02an.getITER();
alpha = g02an.getALPHA();


Nearest correlation matrix with fixed leading block
  1.0000  -0.3250   0.1881   0.4606   0.0051  -0.4887  -0.0579  -0.1271 
 -0.3250   1.0000   0.2048   0.1948   0.3245   0.2183   0.2294   0.3391 
  0.1881   0.2048   1.0000  -0.1060   0.6124   0.2211  -0.4936   0.7202 
  0.4606   0.1948  -0.1060   1.0000   0.2432   0.0101   0.5160  -0.2567 
  0.0051   0.3245   0.6124   0.2432   1.0000   0.5320  -0.2634   0.7949 
 -0.4887   0.2183   0.2211   0.0101   0.5320   1.0000   0.0393   0.4769 
 -0.0579   0.2294  -0.4936   0.5160  -0.2634   0.0393   1.0000  -0.3185 
 -0.1271   0.3391   0.7202  -0.2567   0.7949   0.4769  -0.3185   1.0000 


jobvl = "N";
jobvr = "N";
n = X[0].length;
lda = X.length;
wr = new double[n];
wi = new double[n];
ldvl = 1;
vl = new double[ldvl];
ldvr = 1;
vr = new double[ldvr];
lwork = 3 * n;
work = new double[lwork];
info = 0;
f08na.eval(jobvl, jobvr, n, X1d, lda, wr, wi, vl, ldvl, vr, ldvr, work, lwork, info);
Arrays.sort(wr);


Sorted eigenvalues of X:   0.0000   0.1375   0.2744   0.3804   0.7768   1.6263   1.7689   3.0356 
Value of alpha returned: 0.2003


Fixing Arbitrary Elements

\[X = \large \alpha T+(1-\alpha)G, \quad T = H \circ G, \quad h_{ij} \in [0,1]\]

Alternating Projections

Alternating Projections with Anderson Acceleration

More on using the NAG Library for Java:

https://www.nag.com/content/nag-library-for-java