//Function to generate a single list of two matrices (train or test), given an index
// [[Rcpp::export]]
Rcpp::List MatSplit( const arma::mat & A, const arma::mat & B, const arma::uvec & splitind){
arma::mat tA = A.rows(splitind);
arma::mat tB = B.rows(splitind);
return Rcpp::List::create(Rcpp::Named("A")=tA,
Rcpp::Named("B")=tB);
}
// this function sample the loading parameters considering constant
// observational variance.
// [[Rcpp::export]]
arma::mat SampleDfmLoads(arma::mat y, arma::mat factors, arma::vec psi,
int s, double c0)
{
/**
* The data matrix 'y' is (T \times q).
* Note that the factors matrix is (T+h \times k). In the models considered
* in the dissertation, h > s. This means that we always have the
* VAR order, 'h', greater than the number of dynamic factors, 's', in the
* observational equation.
* The argument 's' is the order of the dynamic factors present in the
* observational equation.
* The prior mean is set to zero.
*/
int T = y.n_rows;
int q = y.n_cols;;
int k = factors.n_cols;
int TpH = factors.n_rows;
int h = TpH - T;
if (h < s+1){
throw std::range_error(
"Argument 's' greater than or equal to factors' VAR order in SampleDfmLoads.cpp"
);
}
arma::mat I_q = eye(q, q);
// std::cout << "\nh = " << h << "\n";
arma::mat Xlambda;
Xlambda = factors.rows(h, TpH-1);
// std::cout << "\nNumber of rows in Xlambda is " << Xlambda.n_rows << "\n";
if (s > 0){
for (int i = 1; i <= s; i++){
Xlambda = arma::join_rows(Xlambda, factors.rows(h-i, TpH-i-1));
}
}
// posterior variance
arma::mat Eigvec;
arma::vec eigval;
arma::eig_sym(eigval, Eigvec, arma::symmatu(Xlambda.t() * Xlambda));
arma::mat kronEig = kron(I_q, Eigvec);
arma::vec L1eigval = 1.0/(arma::kron((1.0/psi), eigval) + 1/c0);
arma::mat L1 = kronEig * diagmat(L1eigval) * kronEig.t();
// posterior mean
arma::vec yStar(y.begin(), T*q);
arma::vec l1 = L1 * (arma::kron(arma::diagmat(1.0/psi), Xlambda.t()) * yStar);
arma::mat l1Mat(l1.begin(), k*(s+1), q); // mean in matrix form
// random generation
arma::vec vecnorm = sqrt(L1eigval) % randn(q*k*(s+1), 1);
arma::mat LambdaBar(vecnorm.begin(), k*(s+1), q, false);
LambdaBar = l1Mat + Eigvec * LambdaBar;
return LambdaBar.t();
}
// [[Rcpp::export]]
arma::mat BeQTL2(const arma::mat & A, const arma::mat & B, const arma::umat & Bootmat){
int bsi= Bootmat.n_rows;
arma::mat C(A.n_cols*B.n_cols,Bootmat.n_rows);
arma::mat tC(A.n_rows,B.n_rows);
for(int i=0; i<bsi; i++){
tC = cor(A.rows(Bootmat.row(i)),B.rows(Bootmat.row(i)));
C.col(i) = vectorise(tC,0);
}
C.elem(find_nonfinite(C)).zeros();
return reshape(median(C,1),A.n_cols,B.n_cols);
}
/******************************************************************
* 函数功能：几何校正需要调用的函数
*
*
*/
arma::mat centering(arma::mat &x){
arma::mat tmp = -mean(x.rows(0, 1), 1);
arma::mat tmp2(2,2);
tmp2.eye();
arma::mat tmp1 = join_horiz(tmp2, tmp);
arma::mat v;
v << 0 << 0 << 1 << arma::endr;
arma::mat T = join_vert(tmp1, v);
//T.print("T =");
arma::mat xm = T * x;
//xm.print("xm =");
//at least one pixel apart to avoid numerical problems
//xm.print("xm =");
double std11 = arma::stddev(xm.row(0));
//cout << "std11:" << std11 << endl;
double std22 = stddev(xm.row(1));
//cout << "std22:" << std22 << endl;
double std1 = std::max(std11, 1.0);
double std2 = std::max(std22, 1.0);
arma::mat S;
S << 1/std1 << 0 << 0 << arma::endr
<< 0 << 1/std2 << 0 << arma::endr
<< 0 << 0 << 1 << arma::endr;
arma::mat C = S * T ;
//C.print("C =");
return C;
}
// **********************************************************//
// Calculate Dyadic statistics //
// **********************************************************//
// [[Rcpp::export]]
arma::cube degreestat (arma::cube cache, arma::mat intervals_d, int a, int A, arma::mat pd) {
int nIP = pd.n_cols;
arma::cube out = arma::zeros<arma::cube>(A, nIP, 6);
for (unsigned int i = 0; i < 3; i++) {
int mins = intervals_d(i, 0)-1;
int maxs = intervals_d(i, 1)-1;
arma::rowvec sendr = arma::zeros<arma::rowvec>(nIP);
arma::mat receiver = arma::zeros<arma::mat>(A, nIP);
arma::mat pdnew = pd.rows(mins, maxs);
for (int r = 0; r < A; r++) {
arma::colvec docsar = cache(arma::span(a), arma::span(r), arma::span(mins, maxs));
sendr += docsar.t() * pdnew;
for (int h = 0; h < A; h++) {
arma::colvec docsra = cache(arma::span(h), arma::span(r), arma::span(mins, maxs));
receiver.row(r) += docsra.t() * pdnew;
}
}
for (int IP = 0; IP < nIP; IP++) {
for (int r = 0; r < A; r++) {
out(r, IP, i) = sendr[IP];
out(r, IP, i+3) = receiver(r,IP);
}
}
}
return out;
}
//Script that takes two matrices, performs bootstrapped correlation, and returns the median
// [[Rcpp::export]]
arma::mat BeQTL(const arma::mat & A, const arma::mat & B, const arma::umat & Bootmat){
int bsi= Bootmat.n_rows;
Rcpp::Rcout<<"Starting Bootstrap!"<<std::endl;
arma::mat C(A.n_cols*B.n_cols,Bootmat.n_rows);
arma::mat tA(A.n_rows,A.n_cols);
arma::mat tB(B.n_rows,B.n_cols);
arma::mat tC(A.n_rows,B.n_rows);
for(int i=0; i<bsi; i++){
tA = A.rows(Bootmat.row(i));
tB = B.rows(Bootmat.row(i));
tC = cor(tA,tB);
C.col(i) = vectorise(tC,0);
}
C.elem(find_nonfinite(C)).zeros();
return reshape(median(C,1),A.n_cols,B.n_cols);
}
arma::colvec computeBetaJ_cpp(arma::colvec y, arma::mat X, int j, int m, int adjFinSample) {
int bigT = X.n_rows;
int numThrow = ceil((double)m / 2);
if (adjFinSample == 0) numThrow = m ;
mat XSparse; colvec ySparse;
XSparse.zeros(bigT - numThrow, X.n_cols); ySparse.zeros(bigT - numThrow);
if (j < 2) {
XSparse.rows(0, bigT - numThrow - 1) = X.rows(numThrow, bigT - 1);
ySparse.rows(0, bigT - numThrow - 1) = y.rows(numThrow, bigT - 1);
} else {
XSparse.rows(0, j - 2) = X.rows(0, j - 2); ySparse.rows(0, j - 2) = y.rows(0, j - 2);
XSparse.rows(j - 1, bigT - numThrow - 1) = X.rows(j + numThrow - 1, bigT - 1);
ySparse.rows(j - 1, bigT - numThrow - 1) = y.rows(j + numThrow - 1, bigT - 1);
}
colvec beta = runOLSFast_cpp(ySparse, XSparse);
return(beta);
}
void
HMM::computeXiCached() {
arma::mat temp = B_.rows(1,T_-1) % beta_.cols(1,T_-1).t();
for(unsigned int i = 0; i < N_; ++i) {
xi_.slice(i) = temp %
(alpha_(i,arma::span(0, T_-2)).t() * A_.row(i));
}
}
static arma::vec s_recall(arma::mat &runMatrix, Qrels &qrels, int rank){
// Use a greedy approach to find the max subtopics at rank k
// Initialize working variables
int numOfSubtopics = int(*qrels.subtopics.rbegin());
int numOfRows = min(rank, qrels.numOfRelDocs);
arma::vec maxSubtopics = arma::zeros(rank);
arma::rowvec seenSubtopics = arma::zeros<arma::rowvec>(numOfSubtopics);
arma::vec tmpVector;
set<int> idealRankList;
set<int>::iterator it;
// Greedy approach searches for the best document at each rank
for(int i = 0; i < numOfRows; i++){
int maxNewSubtopics = 0;
int pickedDoc = -1;
// Iterate through the set of relevant documents to find
// the best document
for(int j = 0; j < qrels.matrix.n_rows; j++){
// Ignore the document already picked
it = idealRankList.find(j);
if(it != idealRankList.end() )
continue;
// Compute the number of new subtopics the document contains
int numOfNewSubtopics = arma::sum((qrels.matrix.row(j) + seenSubtopics) >
arma::zeros<arma::vec>(numOfSubtopics));
// Keep track of the best document/ max number of subtopics
if(numOfNewSubtopics > maxNewSubtopics){
maxNewSubtopics = numOfNewSubtopics;
pickedDoc = j;
}
}
// Add the best document to the ideal rank list
// and keep track of subtopics seen
seenSubtopics += qrels.matrix.row(pickedDoc);
idealRankList.insert(pickedDoc);
maxSubtopics(i) = arma::sum(seenSubtopics >
arma::zeros<arma::vec>(numOfSubtopics));
}
if(numOfRows < rank){
for(int i=numOfRows; i < rank; i++)
maxSubtopics(i) = maxSubtopics(numOfRows - 1);
}
// Consider only the top 'rank' number of documents
arma::vec s_recall = arma::zeros(rank);
for(int i=0; i < rank; i++){
arma::mat matrix = runMatrix.rows(0,i);
double retSubtopics = arma::sum(arma::sum(matrix) >
arma::zeros<arma::vec>(numOfSubtopics));
s_recall(i) = (retSubtopics/maxSubtopics(i));
}
return s_recall;
}
//[[Rcpp::export]]
double computeSStat_cpp(arma::colvec beta, arma::mat invS, arma::colvec y, arma::mat X,
int j, int m) {
mat newX = X.rows(j - 1, j + m - 2); colvec newY = y.rows(j - 1, j + m - 2);
mat A = trans(newX) * invS * (newY - newX * beta);
mat V = trans(newX) * invS * newX;
mat S = trans(A) * inv(V) * A;
double s = S(0, 0);
return(s);
}
/*******************************************************************
* 函数功能：几何校正需要调用的函数
*
*
*/
arma::mat toAffinity(arma::mat &f){
arma::mat A;
arma::mat v;
v << 0 << 0 << 1 << arma::endr;
int flag = f.n_rows;
switch(flag){
case 6:{ // oriented ellipses
arma::mat T = f.rows(0, 1);
arma::mat tmp = join_horiz(f.rows(2, 3), f.rows(4, 5));
arma::mat tmp1 = join_horiz(tmp, T);
A = join_vert(tmp1, v);
break;}
case 4:{ // oriented discs
arma::mat T = f.rows(0, 1);
double s = f.at(2,0);
double th = f.at(3,0);
arma::mat S = arma::randu<arma::mat>(2,2);
/*S.at(0, 0) = s*cos(th);
S.at(0, 1) = -s*sin(th);
S.at(1, 0) = s*sin(th);
S.at(1, 1) = s*cos(th);*/
S << s*cos(th) << -s*sin(th) << arma::endr
<< s*sin(th) << s*cos(th) << arma::endr;
arma::mat tmp1 = join_horiz(S, T);
A = join_vert(tmp1, v);
//A.print("A =");
break;}
/*case 3:{ // discs
mat T = f.rows(0, 1);
mat s = f.row(2);
int th = 0 ;
A = [s*[cos(th) -sin(th) ; sin(th) cos(th)], T ; 0 0 1] ;
}
case 5:{ // ellipses
mat T = f.rows(0, 1);
A = [mapFromS(f(3:5)), T ; 0 0 1] ;
}*/
default:
std::cout << "出错啦！" << std::endl;
break;
}
return A;
}
// **********************************************************//
// Calculate Triadic statistics //
// **********************************************************//
// [[Rcpp::export]]
arma::cube triadicstat (arma::cube cache, arma::mat intervals_d, int a, int A, arma::mat pd) {
int nIP = pd.n_cols;
arma::cube out = arma::zeros<arma::cube>(A, nIP, 36);
int it = 0;
for (unsigned int i = 0; i < 3; i++) {
for (unsigned int j = 0; j < 3; j++) {
int mins1 = intervals_d(i, 0)-1;
int maxs1 = intervals_d(i, 1)-1;
int mins2 = intervals_d(j, 0)-1;
int maxs2 = intervals_d(j, 1)-1;
arma::mat tsend = arma::zeros<arma::mat>(A, nIP);
arma::mat treceive = arma::zeros<arma::mat>(A, nIP);
arma::mat sibling = arma::zeros<arma::mat>(A, nIP);
arma::mat cosibling = arma::zeros<arma::mat>(A, nIP);
arma::mat pdnew1 = pd.rows(mins1, maxs1);
arma::mat pdnew2 = pd.rows(mins2, maxs2);
for (int r = 0; r < A; r++) {
for (int h = 0; h < A; h++) {
arma::colvec docsah = cache(arma::span(a), arma::span(h), arma::span(mins1, maxs1));
arma::colvec docsrh = cache(arma::span(r), arma::span(h), arma::span(mins2, maxs2));
arma::colvec docsha = cache(arma::span(h), arma::span(a), arma::span(mins1, maxs1));
arma::colvec docshr = cache(arma::span(h), arma::span(r), arma::span(mins2, maxs2));
tsend.row(r) += (docsah.t() * pdnew1) % (docshr.t() * pdnew2);
treceive.row(r) += (docsha.t() * pdnew1) % (docsrh.t() * pdnew2);
sibling.row(r) += (docsha.t() * pdnew1) % (docshr.t() * pdnew2);
cosibling.row(r) += (docsah.t() * pdnew1) % (docsrh.t() * pdnew2);
}
}
for (int IP = 0; IP < nIP; IP++) {
for (int r = 0; r < A; r++) {
out(r, IP, it) = tsend(r, IP);
out(r, IP, it+9) = treceive(r,IP);
out(r, IP, it+18) = sibling(r, IP);
out(r, IP, it+27) = cosibling(r,IP);
}
}
it +=1;
}
}
arma::cube out2 = arma::zeros<arma::cube>(A, nIP, 12);
for (int t = 0; t < 4; t++) {
int add = 9*t;
for (int IP = 0; IP < nIP; IP++) {
for (int r = 0; r < A; r++) {
out2(r, IP, 3*t+0) = out(r, IP, add+0);
out2(r, IP, 3*t+1) = out(r, IP, add+1) + out(r, IP, add+3)+ out(r, IP, add+4);
out2(r, IP, 3*t+2) = out(r, IP, add+2) + out(r, IP, add+5)+ out(r, IP, add+6)+ out(r, IP, add+7)+ out(r, IP, add+8);
}
}
}
return out2 / 10;
}
// This piece of code computes the flowlength before taking into account
// the dimensions of pixels/slope.
//[[Rcpp::export]]
double fl_internal(arma::mat m) {
uword ny = m.n_cols;
uword nx = m.n_rows;
rowvec flcol = zeros(1, ny);
for ( uword r=0; r<nx; r++ ) {
rowvec a = sum(cumprod(m.rows(r, nx - 1), 0), 0);
flcol += a;
}
return( accu(flcol)/((double)nx * (double)ny) );
}
void RNN<
LayerTypes, OutputLayerType, InitializationRuleType, PerformanceFunction
>::Gradient(const arma::mat& /* unused */,
const size_t i,
arma::mat& gradient)
{
if (gradient.is_empty())
{
gradient = arma::zeros<arma::mat>(parameter.n_rows, parameter.n_cols);
}
else
{
gradient.zeros();
}
Evaluate(parameter, i, false);
arma::mat currentGradient = arma::mat(gradient.n_rows, gradient.n_cols);
NetworkGradients(currentGradient, network);
const arma::mat input = arma::mat(predictors.colptr(i), predictors.n_rows,
1, false, true);
// Iterate through the input sequence and perform the feed backward pass.
for (seqNum = seqLen - 1; seqNum >= 0; seqNum--)
{
// Load the network activation for the upcoming backward pass.
LoadActivations(input.rows(seqNum * inputSize, (seqNum + 1) *
inputSize - 1), network);
// Perform the backward pass.
if (seqOutput)
{
arma::mat seqError = error.unsafe_col(seqNum);
Backward(seqError, network);
}
else
{
Backward(error, network);
}
// Link the parameters and update the gradients.
LinkParameter(network);
UpdateGradients<>(network);
// Update the overall gradient.
gradient += currentGradient;
if (seqNum == 0) break;
}
}
arma::colvec computeTestStatDistribution_cpp(arma::colvec y, arma::mat X, int breakDate,
int m, int adjFinSample, arma::mat invS) {
int bigT = X.n_rows;
colvec sJ = zeros(breakDate - m + 1);
for (int j = 0; j < (breakDate - m + 1); j++) {
colvec betaJ = computeBetaJ_cpp(y.rows(0, bigT - 1 - m), X.rows(0, bigT - 1 - m),
j + 1, m, adjFinSample);
sJ(j) = computeSStat_cpp(betaJ, invS, y, X, j + 1, m);
// if (j == 44) {
// Rcout << "betaJ = "<< betaJ << "sJ(j) = " << sJ(j) << endl;
// }
}
return(sJ);
}
/**
* Remove a certain set of rows in a matrix while copying to a second matrix.
*
* @param input Input matrix to copy.
* @param rowsToRemove Vector containing indices of rows to be removed.
* @param output Matrix to copy non-removed rows into.
*/
void mlpack::math::RemoveRows(const arma::mat& input,
const std::vector<size_t>& rowsToRemove,
arma::mat& output)
{
const size_t nRemove = rowsToRemove.size();
const size_t nKeep = input.n_rows - nRemove;
if (nRemove == 0)
{
output = input; // Copy everything.
}
else
{
output.set_size(nKeep, input.n_cols);
size_t curRow = 0;
size_t removeInd = 0;
// First, check 0 to first row to remove.
if (rowsToRemove[0] > 0)
{
// Note that this implies that n_rows > 1.
output.rows(0, rowsToRemove[0] - 1) = input.rows(0, rowsToRemove[0] - 1);
curRow += rowsToRemove[0];
}
// Now, check i'th row to remove to (i + 1)'th row to remove, until i is the
// penultimate row.
while (removeInd < nRemove - 1)
{
const size_t height = rowsToRemove[removeInd + 1] -
rowsToRemove[removeInd] - 1;
if (height > 0)
{
output.rows(curRow, curRow + height - 1) =
input.rows(rowsToRemove[removeInd] + 1,
rowsToRemove[removeInd + 1] - 1);
curRow += height;
}
removeInd++;
}
// Now that i is the last row to remove, check last row to remove to last
// row.
if (rowsToRemove[removeInd] < input.n_rows - 1)
{
output.rows(curRow, nKeep - 1) = input.rows(rowsToRemove[removeInd] + 1,
input.n_rows - 1);
}
}
}
// gradients -------------------------------------------------------------------
//' @title Gradient step for Latent Factors
//' @param x Either a single row or single column of X, the ratings matrix.
//' @param z A single matrix from the covariates array, associated with the
//' either a single row or column of X.
//' @param p_i The latent factors associated with a single user or track.
//' @param Q The latent factors associated with either all tracks or all users,
//' depending on the type of latent factor in p_i.
//' @param beta The learned regression coefficients.
//' @param lambda The regularization parameter for the current latent factor.
//' @param batch_samples The proportion of the observed entries to sample in the
//' gradient for each factor in the gradient descent.
//' @param gamma The step-size in the gradient descent.
//' @return The update latent factor for the current user / track.
//' @export
// [[Rcpp::export]]
arma::vec update_factor(arma::vec x, arma::mat z, arma::vec p_i, arma::mat Q,
arma::vec beta, double lambda, double batch_samples,
double gamma) {
// subset to SGD rows with observed entries
arma::uvec obs_ix = arma::conv_to<arma::uvec>::from(arma::find_finite(x));
arma::mat Q_obs = Q.rows(obs_ix);
arma::vec x_obs = x(obs_ix);
arma::uvec batch_ix = get_batch_ix(x_obs.n_elem, batch_samples);
if(batch_ix.n_elem > 0) {
x_obs = x_obs(batch_ix);
Q_obs = Q_obs.rows(batch_ix);
}
arma::vec resid = x_obs - Q_obs * p_i;
arma::vec p_i_grad = 2 * (lambda * p_i - Q_obs.t() * resid);
return p_i - gamma * p_i_grad;
}
// [[Rcpp::export]]
List PCspatregMCMC(const arma::vec& y, const arma::mat& X, const arma::mat& K, const arma::uvec& sampleIndex,
const arma::vec& betaMean, const arma::mat& betaSig, const double& phiScale, const int& burn, const int& iter) {
int na = K.n_cols;
int nsite = X.n_rows;
int nb = X.n_cols;
int ns = y.n_elem;
arma::uvec idx = sampleIndex-1;
arma::mat Xsmp = X.rows(idx);
arma::mat Ksmp = K.rows(idx);
arma::mat betaStor(iter, nb, fill::zeros);
arma::mat alphaStor(iter, na, fill::zeros);
arma::vec phiStor(iter, fill::zeros);
arma::vec sigStor(iter, fill::zeros);
arma::mat predStor(iter, nsite);
// Beta items
arma::mat betaPrec = betaSig.i();
arma::mat V_beta_inv(nb, nb);
arma::vec v_beta(nb);
// Alpha items
arma::mat I(na,na, fill::eye);
arma::mat V_alpha_inv(na, na);
arma::vec v_alpha(na);
// phi items
arma::vec Kbar(ns);
double V_phi_inv;
double v_phi;
// Initial values
arma::vec beta(nb);
beta = solve(Xsmp.t() * Xsmp, Xsmp.t()*y);
double tau = (ns-1)/as_scalar((y - Xsmp*beta).t()*(y - Xsmp*beta));
double phi = 0;
arma::vec alpha(na, fill::zeros);
for(int i=0; i<iter+burn; i++){
// update beta
V_beta_inv = tau*Xsmp.t()*Xsmp + betaPrec;
v_beta = tau * Xsmp.t() * (y - phi*Ksmp*alpha) + betaPrec*betaMean;
beta = GCN(V_beta_inv, v_beta);
if(i>=burn){betaStor.row(i-burn) = beta.t();}
// update alpha
V_alpha_inv = phi*phi*tau*Ksmp.t()*Ksmp + I;
v_alpha = phi*tau*Ksmp.t()*(y-Xsmp*beta);
alpha = GCN(V_alpha_inv, v_alpha);
if(i>=burn){alphaStor.row(i-burn) = phi*alpha.t();}
// update phi
Kbar = Ksmp*alpha;
V_phi_inv = tau*as_scalar(Kbar.t()*Kbar) + 1/(phiScale*phiScale);
v_phi = tau*dot(Kbar, y-Xsmp*beta);
phi = as<double>(rnorm(1, v_phi/V_phi_inv, 1/sqrt(V_phi_inv)));
if(i>=burn) phiStor(i-burn) = phi;
// update tau
tau = as<double>(rgamma(1, ns/2, as_scalar((y-Xsmp*beta-phi*Ksmp*alpha).t()*(y-Xsmp*beta-phi*Ksmp*alpha))/2));
if(i>=burn) sigStor(i-burn) = 1/sqrt(tau);
// make prediction
if(i>=burn){
predStor.row(i-burn) = (X*beta + phi*K*alpha).t();
}
}
return Rcpp::List::create(
Rcpp::Named("beta") = betaStor,
Rcpp::Named("alpha") = alphaStor,
Rcpp::Named("phi")=phiStor,
Rcpp::Named("sigma")=sigStor,
Rcpp::Named("pred")=predStor
);
}
// [[Rcpp::export]]
Rcpp::List getWEXPcutoff(arma::mat data, arma::mat subdata, arma::mat Y, arma::mat subY, int N, arma::mat RT_out, double predictTime, arma::vec resid_sco, double fitvar, arma::colvec cutoffs){
//create dataD
arma::mat dataDuns = data.rows(find(data.col(1)==1));
arma::mat dataD = dataDuns.rows(sort_index(dataDuns.col(0)));
int n = data.n_rows, nD = dataD.n_rows, np = Y.n_cols, ncuts = subdata.n_rows;
//guide
colvec times = data.col(0);
// status= data.col(1);
// Dtimes = dataD.col(0);
// weights = data.col(4);
// Dweights = dataD.col(4);
uvec tmpind = find((data.col(0) <= predictTime)%data.col(1)); // indices of (data$times<=predict.time)&(data$status==1)
mat myempty(1,1);
uvec tmpindT = conv_to<uvec>::from(CSumI(times.elem(tmpind), 4, dataD.col(0), myempty, FALSE));
colvec rrk = exp(data.col(6)); //data.col(6) is data$linearY
// build riskmat
mat riskmat(n, nD);
mat::iterator riskmat_it = riskmat.begin();
for(colvec::iterator j = dataD.begin_col(0); j != dataD.end_col(0); j++){
for( colvec::iterator i = data.begin_col(0); i != data.end_col(0); i++){
*riskmat_it = *i >= *j; riskmat_it++;
}
}
//s0 and s1
colvec s0 = riskmat.t()*(rrk%data.col(4));
colvec s1 = riskmat.t()*trans(Vec2Mat(rrk%data.col(4), np)%Y.t());
//haz0 and cumhaz0
colvec haz0 = dataD.col(4)/sum(riskmat%trans(Vec2Mat(rrk%data.col(4), nD))).t();
colvec cumhaz0 = cumsum(haz0);
colvec ptvec(1); ptvec(0) = predictTime;
colvec cumhaz_t0 = CSumI(ptvec, 4, dataD.col(0), haz0, TRUE);
//Wexp
colvec Wexp_beta = resid_sco*fitvar*N;
colvec WexpLam1(n); WexpLam1.zeros(n);
WexpLam1(tmpind) = N/s0(tmpindT - 1);
WexpLam1 = WexpLam1 - CSumI( myPmin(data.col(0), predictTime), 4, dataD.col(0), haz0/s0, TRUE)%rrk*N;
colvec WexpLam2 = Wexp_beta*CSumI(ptvec, 4, dataD.col(0), haz0%s1/trans(Vec2Mat(s0, np)), TRUE);
colvec WexpLam = WexpLam1 - WexpLam2;
//Fyk = Pr(Sy < c)
colvec Fyk = CSumI( cutoffs, 4, data.col(6), data.col(4), TRUE)/sum(data.col(4));
colvec dFyk(Fyk.n_elem); dFyk(0) = 0;
dFyk(span(1, Fyk.n_elem - 1)) = Fyk(span(0, Fyk.n_elem-2));
dFyk = Fyk - dFyk;
colvec Sy = subdata.col(5);
colvec Syall = data.col(5);
colvec St0_Fyk = cumsum(Sy%dFyk);
double St0 = max(St0_Fyk);
colvec St0_Syk = St0 - St0_Fyk;
//
mat Wexp_Cond_Stc = -Vec2Mat(Sy%exp(subdata.col(6)), n)%(trans(Vec2Mat(WexpLam, ncuts)) +as_scalar(cumhaz_t0)*Wexp_beta*subY.t());
mat tmpmat = conv_to<mat>::from(trans(Vec2Mat(data.col(6), ncuts)) > Vec2Mat(cutoffs, n));
mat Wexp_Stc = trans(CSumI(cutoffs, 0, subdata.col(6), Wexp_Cond_Stc.t()%Vec2Mat(dFyk, n).t(), TRUE)) + trans(Vec2Mat(Syall,ncuts))%tmpmat - Vec2Mat(St0_Syk, n);
colvec Wexp_St = sum(trans(Wexp_Cond_Stc)%trans(Vec2Mat(dFyk, n))).t() + Syall - St0;
mat Wexp_Fc = 1-tmpmat - Vec2Mat(Fyk, n);
//assemble for classic performance measures, given linear predictor
List out(8);
out[0] = -Wexp_Cond_Stc;
out[1] = Wexp_Fc;
mat Wexp_St_mat = Vec2Mat(Wexp_St, ncuts).t();
out[2] = (-Wexp_St_mat%Vec2Mat(RT_out.col(3), n) + Wexp_Stc)/St0;
out[3] = (Wexp_St_mat%Vec2Mat(RT_out.col(4), n) -Wexp_Fc - Wexp_Stc)/(1-St0);
out[4] = -Wexp_St;
out[5] = (Wexp_St_mat - Wexp_Stc - Vec2Mat(RT_out.col(6), n)%Wexp_Fc)/Vec2Mat(Fyk, n);
out[6] = (Vec2Mat(RT_out.col(5)-1, n)%Wexp_Fc - Wexp_Stc)/Vec2Mat(1-Fyk, n);
out[7] = Wexp_beta;
return out;
}
//' @export
// [[Rcpp::export]]
Rcpp::List affineObservationStateHandler_affineContracts(const arma::mat& stateMat, const Rcpp::List& modelParameters, const int iterCount){
// In state mat, additionally, to state values, we carry the past filtered state
// because it is necessary to calculate effects of stock return observation
int Nf = stateMat.n_rows/2;
// Evaluate divergence prices
arma::cube cfCoeffs = Rcpp::as<arma::cube>(modelParameters["cfCoeffs"]);
arma::vec pVecUnique = Rcpp::as<arma::vec>(modelParameters["pVecUnique"]);
arma::vec tVecUnique = Rcpp::as<arma::vec>(modelParameters["tVecUnique"]);
arma::vec pVec = Rcpp::as<arma::vec>(modelParameters["pVec"]);
arma::vec tVec = Rcpp::as<arma::vec>(modelParameters["tVec"]);
arma::cube divPrices = divergenceSwapRateCpp(pVecUnique, cfCoeffs, stateMat.rows(0,Nf-1).t());
arma::cube skewPrices = skewnessSwapRateCpp(pVecUnique, cfCoeffs, stateMat.rows(0,Nf-1).t());
// create return matrix
arma::mat yhat(pVec.n_elem,stateMat.n_cols);
// Cycle over state variable columns
for(unsigned int kcol=0; kcol < stateMat.n_cols; kcol++){
// Cycle through the representation of the contract specification matrix and construct final prices from priced single instruments
for(unsigned int prow=0; prow < pVec.n_elem; prow++){
// find p and t values in the unique vectors to know what to pick
double loc_p = pVec(prow);
double loc_t = tVec(prow);
arma::vec loc_p_vec(pVecUnique.n_elem);
loc_p_vec.fill(loc_p);
arma::vec loc_t_vec(tVecUnique.n_elem);
loc_t_vec.fill(loc_t);
arma::uvec which_p = find(loc_p_vec == pVecUnique);
arma::uvec which_t = find(loc_t_vec == tVecUnique);
// Rcout << "loc_p= " << loc_p << ", loc_t= " << loc_t << "\n";
// pVecUnique.print("pVecUnique");
// which_p.print("which_p");
// tVecUnique.print("tVecUnique");
// which_t.print("which_t");
// pick and calculate necessary affine swap rate
double loc_div_price = divPrices(which_p(0L),which_t(0L),kcol);
double loc_skew_price = skewPrices(which_p(0L),which_t(0L),kcol);
if(loc_p == 0.0){
yhat(prow, kcol) = loc_div_price;
} else if(loc_p == 1.0){
yhat(prow, kcol) = loc_skew_price/loc_div_price;
} else {
yhat(prow, kcol) = (loc_skew_price - (1.0 - 2.0*loc_p)/(loc_p*(loc_p-1.0))*loc_div_price) / (loc_div_price + 1.0/(loc_p*(loc_p-1.0)));
}
}
}
// Handle the noise covariance matrix. The stock ``observation'' noise is
// uncorrelated with portfolio observation noise.
arma::mat obsNoiseMat(pVec.n_elem,pVec.n_elem,arma::fill::zeros);
//
// // extract observation noise params
// arma::vec bVec = Rcpp::as<arma::vec>(modelParameters["bVec"]);
// arma::vec cVec = Rcpp::as<arma::vec>(modelParameters["cVec"]);
// // double spotVol = arma::accu(stateMat.col(0));
// double spotVol = arma::accu(stateMat.submat(0,0,Nf-1,0));
// obsNoiseMat(arma::span(1,obsNoiseMat.n_rows-1),arma::span(1,obsNoiseMat.n_cols-1)) = divModelObsNoiseMat(cVec,bVec,spotVol,tVecUnique,U);
SEXP divBigMat_SEXP(modelParameters["divNoiseCube"]);
arma::cube divBigMat = as<arma::cube>(divBigMat_SEXP);
// var-cov matrix scaling
arma::vec errSdParVec = as<arma::vec>(modelParameters["errSdParVec"]);
obsNoiseMat(arma::span(0,obsNoiseMat.n_rows-1),arma::span(0,obsNoiseMat.n_cols-1)) = errSdParVec(0) * divBigMat.slice(iterCount);
// Initialize return list
Rcpp::List res = Rcpp::List::create(Rcpp::Named("yhat") = yhat, Rcpp::Named("obsNoiseMat") = obsNoiseMat);
return res;
}