/**
* Applies rank transform to each of the columns of <code>matrix</code> using the current <code>
* rankingAlgorithm</code>
*
* @param matrix matrix to transform
* @return a rank-transformed matrix
*/
private RealMatrix rankTransform(final RealMatrix matrix) {
RealMatrix transformed = null;
if (rankingAlgorithm instanceof NaturalRanking
&& ((NaturalRanking) rankingAlgorithm).getNanStrategy() == NaNStrategy.REMOVED) {
final Set<Integer> nanPositions = new HashSet<Integer>();
for (int i = 0; i < matrix.getColumnDimension(); i++) {
nanPositions.addAll(getNaNPositions(matrix.getColumn(i)));
}
// if we have found NaN values, we have to update the matrix size
if (!nanPositions.isEmpty()) {
transformed =
new BlockRealMatrix(
matrix.getRowDimension() - nanPositions.size(), matrix.getColumnDimension());
for (int i = 0; i < transformed.getColumnDimension(); i++) {
transformed.setColumn(i, removeValues(matrix.getColumn(i), nanPositions));
}
}
}
if (transformed == null) {
transformed = matrix.copy();
}
for (int i = 0; i < transformed.getColumnDimension(); i++) {
transformed.setColumn(i, rankingAlgorithm.rank(transformed.getColumn(i)));
}
return transformed;
}
/**
* Computes the Kendall's Tau rank correlation matrix for the columns of the input matrix.
*
* @param matrix matrix with columns representing variables to correlate
* @return correlation matrix
*/
public RealMatrix computeCorrelationMatrix(final RealMatrix matrix) {
int nVars = matrix.getColumnDimension();
RealMatrix outMatrix = new BlockRealMatrix(nVars, nVars);
for (int i = 0; i < nVars; i++) {
for (int j = 0; j < i; j++) {
double corr = correlation(matrix.getColumn(i), matrix.getColumn(j));
outMatrix.setEntry(i, j, corr);
outMatrix.setEntry(j, i, corr);
}
outMatrix.setEntry(i, i, 1d);
}
return outMatrix;
}
public double computeSimilarity(RealMatrix sourceDoc, RealMatrix targetDoc) {
if (sourceDoc.getRowDimension() != targetDoc.getRowDimension()
|| sourceDoc.getColumnDimension() != targetDoc.getColumnDimension()
|| sourceDoc.getColumnDimension() != 1) {
throw new IllegalArgumentException(
"Matrices are not column matrices or not of the same size");
}
double[] source = sourceDoc.getColumn(0);
double[] target = targetDoc.getColumn(0);
double dotProduct = dot(source, target);
double distance = norm(source) * norm(target);
return dotProduct / distance;
}
/**
* Compute a covariance matrix from a matrix whose columns represent covariates.
*
* @param matrix input matrix (must have at least one column and two rows)
* @param biasCorrected determines whether or not covariance estimates are bias-corrected
* @return covariance matrix
* @throws MathIllegalArgumentException if the matrix does not contain sufficient data
*/
protected RealMatrix computeCovarianceMatrix(RealMatrix matrix, boolean biasCorrected)
throws MathIllegalArgumentException {
int dimension = matrix.getColumnDimension();
Variance variance = new Variance(biasCorrected);
RealMatrix outMatrix = new BlockRealMatrix(dimension, dimension);
for (int i = 0; i < dimension; i++) {
for (int j = 0; j < i; j++) {
double cov = covariance(matrix.getColumn(i), matrix.getColumn(j), biasCorrected);
outMatrix.setEntry(i, j, cov);
outMatrix.setEntry(j, i, cov);
}
outMatrix.setEntry(i, i, variance.evaluate(matrix.getColumn(i)));
}
return outMatrix;
}
/**
* Returns a list containing the indices of NaN values in the input array.
*
* @param input the input array
* @return a list of NaN positions in the input array
*/
private void rankTransform(RealMatrix matrix) {
for (int i = 0; i < matrix.getColumnDimension(); i++) {
matrix.setColumn(i, rankingAlgorithm.rank(matrix.getColumn(i)));
}
}