// Qf <- function(par)
private double qF(double[] par, ArrayRealVector y, ArrayRealVector w) {
// fv <- solve((exp(-par[1])*W) + (exp(-par[2])*G),
// (exp(-par[1])*W)%*%as.vector(y))
solver =
new QRDecomposition(
wM.scalarMultiply(FastMath.exp(-par[0]))
.add(gM.scalarMultiply(FastMath.exp(-par[1]))))
.getSolver();
fv = (ArrayRealVector) solver.solve(wM.scalarMultiply(FastMath.exp(-par[0])).operate(y));
// b <- diff(fv, differences=order)
b = MatrixFunctions.diffV(fv, Controls.RW_ORDER);
// DT <- determinant((exp(-par[1])*W) + (exp(-par[2])*G))$modulus
double dt =
new LUD(
wM.scalarMultiply(FastMath.exp(-par[0]))
.add(gM.scalarMultiply(FastMath.exp(-par[1]))))
.getDeterminant();
// f <- -(N/2)*log(2*pi*exp(par[1])) + # 1
tempV = y.subtract(fv);
double f =
-(n / 2) * FastMath.log(2 * FastMath.PI * FastMath.exp(par[0]))
// .5*sum(log(weights))- # 2
+ 0.5 * MatrixFunctions.sumV(MatrixFunctions.logVec(w))
// sum(weights*(y-fv)^2)/(2*exp(par[1])) + # 3
- MatrixFunctions.sumV(w.ebeMultiply(tempV).ebeMultiply(tempV))
/ (2 * FastMath.exp(par[0]))
// (N/2)*log(2*pi) - # 4
+ (n * FastMath.log(2 * FastMath.PI)) / 2
// ((N-order)/2)*log(2*pi*exp(par[2]))- # 5
- ((n - Controls.RW_ORDER) * FastMath.log(2 * FastMath.PI * FastMath.exp(par[1]))) / 2
// sum(b^2)/(2*exp(par[2])) - # 6
- MatrixFunctions.sumV(b.ebeMultiply(b)) / (2 * FastMath.exp(par[1]))
// .5*DT # 7
- 0.5 * dt;
// attributes(f) <- NULL
// Pen <- if (penalty==TRUE) delta[1]*(par[1]-shift[1])^2
// + delta[2]*(par[2]-shift[2])^2 else 0 -f+Pen
double pen = 0;
if (Controls.PENALTY) {
pen =
delta.getEntry(0) * (par[0] - Controls.RW_SHIFT[0]) * (par[0] - Controls.RW_SHIFT[0])
+ delta.getEntry(1)
* (par[1] - Controls.RW_SHIFT[1])
* (par[1] - Controls.RW_SHIFT[1]);
}
// -f+Pen # no penalty yet
return (-f + pen);
}
/**
* The main fitting method of Random Walk smoother.
*
* @param additiveFit - object of AdditiveFit class
* @return residuals
*/
public ArrayRealVector solve(AdditiveFit additiveFit) {
ArrayRealVector y = additiveFit.getZ();
ArrayRealVector w = additiveFit.getW();
int whichDistParameter = additiveFit.getWhichDistParameter();
// if (any(is.na(y)))
for (int i = 0; i < y.getDimension(); i++) {
if (Double.isNaN(y.getEntry(i))) {
// weights[is.na(y)] <- 0
w.setEntry(i, 0.0);
// y[is.na(y)] <- 0
y.setEntry(i, 0.0);
}
}
// N <- length(y)
n = y.getDimension();
// ------------------------------------------------------- BECOMES VERY SLOW HERE
// W <- diag.spam(x=weights) # weights
wM = (BlockRealMatrix) MatrixUtils.createRealDiagonalMatrix(w.getDataRef());
// E <- diag.spam(N)
eM = MatrixFunctions.buildIdentityMatrix(n);
// D <- diff(E, diff = order) # order
dM = MatrixFunctions.diff(eM, Controls.RW_ORDER);
// ------------------------------------------------------- FREEZES HERE
// G <- t(D)%*%D
gM = dM.transpose().multiply(dM);
// logsig2e <- log(sig2e) # getting logs
double logsig2e = FastMath.log(sigmasHash.get(whichDistParameter)[0]);
// logsig2b <- log(sig2b)
double logsig2b = FastMath.log(sigmasHash.get(whichDistParameter)[1]);
// fv <- solve(exp(-logsig2e)*W + exp(-logsig2b)*G,
// (exp(-logsig2e)*W)%*% as.vector(y))
solver =
new QRDecomposition(
wM.scalarMultiply(FastMath.exp(-logsig2e))
.add(gM.scalarMultiply(FastMath.exp(-logsig2b))))
.getSolver();
fv = (ArrayRealVector) solver.solve(wM.scalarMultiply(FastMath.exp(-logsig2e)).operate(y));
// if (sig2e.fix==FALSE && sig2b.fix==FALSE) # both estimated{
if (Controls.SIG2E_FIX) {
if (Controls.SIG2B_FIX) {
// out <- list()
// par <- c(logsig2e, logsig2b)
// out$par <- par
// value.of.Q <- -Qf(par)
valueOfQ = -qF(new double[] {logsig2e, logsig2b}, y, w);
// se <- NULL
se = null;
} else {
// par <- log(sum((D%*%fv)^2)/N)
tempV = (ArrayRealVector) dM.operate(fv);
logsig2b = FastMath.log(MatrixFunctions.sumV(tempV.ebeMultiply(tempV)) / n);
// Qf1 <- function(par) Qf(c(logsig2e, par))
// out<-nlminb(start = par,objective = Qf1,
// lower = c(-20), upper = c(20))
nonLinObj1.setResponse(y);
nonLinObj1.setWeights(w);
nonLinObj1.setLogsig2e(logsig2e);
maxiter = new MaxIter(Controls.BOBYQA_MAX_ITER);
maxeval = new MaxEval(Controls.BOBYQA_MAX_EVAL);
initguess = new InitialGuess(new double[] {logsig2b, logsig2b});
bounds =
new SimpleBounds(
new double[] {-Double.MAX_VALUE, -Double.MAX_VALUE},
new double[] {Double.MAX_VALUE, Double.MAX_VALUE});
obj = new ObjectiveFunction(nonLinObj1);
PointValuePair values =
optimizer.optimize(maxiter, maxeval, obj, initguess, bounds, GoalType.MINIMIZE);
logsig2b = values.getPoint()[0];
if (logsig2b > 20.0) {
logsig2b = 20.0;
valueOfQ = -qF(new double[] {logsig2e, logsig2b}, y, w);
} else if (logsig2b < -20.0) {
logsig2b = -20.0;
valueOfQ = -qF(new double[] {logsig2e, logsig2b}, y, w);
} else {
valueOfQ = -values.getValue();
}
// out$hessian <- optimHess(out$par, Qf1)
// value.of.Q <- -out$objective
// shes <- 1/out$hessian
// se1 <- ifelse(shes>0, sqrt(shes), NA)
// par <- c(logsig2e, out$par)
// names(par) <- c("logsig2e", "logsig2b")
/// out$par <- par
// se <- c(NA, se1)
// System.out.println(logsig2e+" "+logsig2b +" "+qF(new double[]{logsig2e, logsig2b}, y,
// w));
}
} else {
if (Controls.SIG2B_FIX) {
// par <- log(sum(weights*(y-fv)^2)/N)
tempV = y.subtract(fv);
logsig2e = FastMath.log(MatrixFunctions.sumV(tempV.ebeMultiply(tempV).ebeMultiply(w)) / n);
// Qf2 <- function(par) Qf(c(par, logsig2b))
// out <- nlminb(start = par, objective = Qf2,
// lower = c(-20), upper = c(20))
nonLinObj2.setResponse(y);
nonLinObj2.setWeights(w);
nonLinObj2.setLogsig2b(logsig2b);
maxiter = new MaxIter(Controls.BOBYQA_MAX_ITER);
maxeval = new MaxEval(Controls.BOBYQA_MAX_EVAL);
initguess = new InitialGuess(new double[] {logsig2e, logsig2e});
bounds =
new SimpleBounds(
new double[] {-Double.MAX_VALUE, -Double.MAX_VALUE},
new double[] {Double.MAX_VALUE, Double.MAX_VALUE});
obj = new ObjectiveFunction(nonLinObj2);
PointValuePair values =
optimizer.optimize(maxiter, maxeval, obj, initguess, bounds, GoalType.MINIMIZE);
logsig2e = values.getPoint()[0];
// out$hessian <- optimHess(out$par, Qf2)
// value.of.Q <- -out$objective
if (logsig2e > 20.0) {
logsig2e = 20.0;
valueOfQ = -qF(new double[] {logsig2e, logsig2b}, y, w);
} else if (logsig2e < -20.0) {
logsig2e = -20.0;
valueOfQ = -qF(new double[] {logsig2e, logsig2b}, y, w);
} else {
valueOfQ = -values.getValue();
}
// shes <- 1/out$hessian
// se1 <- ifelse(shes>0, sqrt(shes), NA)
// par <- c( out$par, logsig2b)
// names(par) <- c("logsig2e", "logsig2b")
// out$par <- par
// se <- c(se1, NA)
// System.out.println(logsig2e+" "+logsig2b +" "+qF(new double[]{logsig2e, logsig2b}, y,
// w));
} else {
// par <- c(logsig2e <- log(sum(weights*(y-fv)^2)/N),
// logsig2b <-log(sum((D%*%fv)^2)/N))
tempV = y.subtract(fv);
logsig2e = FastMath.log(MatrixFunctions.sumV(w.ebeMultiply(tempV).ebeMultiply(tempV)) / n);
tempV = (ArrayRealVector) dM.operate(fv);
logsig2b = FastMath.log(MatrixFunctions.sumV(tempV.ebeMultiply(tempV)) / n);
nonLinObj.setResponse(y);
nonLinObj.setWeights(w);
// out <- nlminb(start = par, objective = Qf,
// lower = c(-20, -20), upper = c(20, 20))
maxiter = new MaxIter(Controls.BOBYQA_MAX_ITER);
maxeval = new MaxEval(Controls.BOBYQA_MAX_EVAL);
initguess = new InitialGuess(new double[] {logsig2e, logsig2b});
bounds = new SimpleBounds(new double[] {-20.0, -20.0}, new double[] {20.0, 20.0});
obj = new ObjectiveFunction(nonLinObj);
PointValuePair values =
optimizer.optimize(maxiter, maxeval, obj, initguess, bounds, GoalType.MINIMIZE);
logsig2e = values.getPoint()[0];
logsig2b = values.getPoint()[1];
// System.out.println(logsig2e+" "+logsig2b +" "+values.getValue());
// out$hessian <- optimHess(out$par, Qf) !!! Missing in Java
// value.of.Q <- -out$objective
valueOfQ = -values.getValue();
// shes <- try(solve(out$hessian))
// se <- if (any(class(shes)%in%"try-error"))
// rep(NA_real_,2) else sqrt(diag(shes))
}
}
// fv <- solve(exp(-out$par[1])*W + exp(-out$par[2])*G,
// (exp(-out$par[1])*W)%*% as.vector(y))
solver =
new QRDecomposition(
wM.scalarMultiply(FastMath.exp(-logsig2e))
.add(gM.scalarMultiply(FastMath.exp(-logsig2b))))
.getSolver();
fv = (ArrayRealVector) solver.solve(wM.scalarMultiply(FastMath.exp(-logsig2e)).operate(y));
sigmasHash.put(
whichDistParameter, new Double[] {FastMath.exp(logsig2e), FastMath.exp(logsig2b)});
// b <- diff(fv, differences=order)
b = MatrixFunctions.diffV(fv, Controls.RW_ORDER);
// tr1 <- order + sum(b^2)/(exp(out$par[2])) # this always right
// attributes(tr1) <- NULL
double tr1 =
Controls.RW_ORDER + MatrixFunctions.sumV(b.ebeMultiply(b)) / (FastMath.exp(logsig2b));
tempV = null;
return y.subtract(fv);
}