inline ArrayXd lm::Dplus(const ArrayXd& d) {
ArrayXd di(d.size());
double comp(d.maxCoeff() * threshold());
for (int j = 0; j < d.size(); ++j) di[j] = (d[j] < comp) ? 0. : 1./d[j];
m_r = (di != 0.).count();
return di;
}
ArrayXd GoSUM::CModelVariables::hcPoint2ModelPoint(const ArrayXd &x)
{
if ( x.size()!=mvs.size() ) throw "GoSUM::CModelVariables::hcPoint2ModelPoint error: wrong dimension";
int j,dim=int(x.size());
ArrayXd X(dim);
for ( j=0; j<dim; j++ )
{ X(j)=mvs[j].generateSampleValue(x(j)); }
return X;
}
void CMATLAB::matPut(string filename,const ArrayXd &X,string Xname)
{
MATFile *pmat=matOpen(filename,string("w"));
if (!pmat) throw "CMATLAB::exportTo error: matOpen failed";
mxArray *pa=mxCreateDoubleMatrix((int)X.size(),1);
if (!pa) throw "CMATLAB::exportTo error: mxCreateDoubleMatrix failed";
memcpy((void *)(mxGetPr(pa)), (void *)X.data(), X.size()*sizeof(double));
if (!matPutVariable(pmat,string("X"),pa)) throw "CMATLAB::exportTo error: matlab.matPutVariable failed";
mxDestroyArray(pa);
if (!matClose(pmat)) throw "CMATLAB::exportTo error: matlab.matClose failed";
}
SSFPSimple::SSFPSimple(const ArrayXd &flip, const double TR, const ArrayXd &phi) :
SteadyState()
{
m_TR = TR;
m_flip = (flip * M_PI / 180.).replicate(phi.rows(), 1);
m_nphi = phi.size();
m_phi = ArrayXd::Zero(m_flip.size());
int start = 0;
for (int i = 0; i < phi.size(); i++) {
m_phi.segment(start, flip.size()).setConstant(phi[i] * M_PI / 180.);
start += flip.size();
}
}
NOMAD::Point CMADS::ArrayXd2NOMADPoint(const ArrayXd &x)
{
int i,n=int(x.size());
NOMAD::Point p(n);
for ( i=0; i<n; i++ ) p[i]=x(i);
return p;
}
void GoSUM::CModelVariables::setNTuple(const ArrayXd &X,int _at)
{
if ( X.size()!=mvs.size() ) throw "GoSUM::CModelVariables::setNTuple error: bad nTupe size";
int i,N=int(mvs.size());
for ( i=0; i<N; i++ ) mvs[i].setSampleValue(X(i),_at);
}
void CMT::HistogramNonlinearity::setParameters(const ArrayXd& parameters) {
if(parameters.size() != mHistogram.size())
throw Exception("Wrong number of parameters.");
for(int i = 0; i < mHistogram.size(); ++i)
mHistogram[i] = parameters[i];
}
const ArrayXd glmDist::devResid(const ArrayXd &y, const ArrayXd &mu, const ArrayXd &wt) const {
int n = mu.size();
return as<ArrayXd>(::Rf_eval(::Rf_lang4(as<SEXP>(d_devRes),
as<SEXP>(NumericVector(y.data(), y.data() + n)),
as<SEXP>(NumericVector(mu.data(), mu.data() + n)),
as<SEXP>(NumericVector(wt.data(), wt.data() + n))
), d_rho));
}
//@{
double gammaDist::aic (const ArrayXd& y, const ArrayXd& n, const ArrayXd& mu,
const ArrayXd& wt, double dev) const {
double nn(wt.sum());
double disp(dev/nn);
double ans(0), invdisp(1./disp);
for (int i = 0; i < mu.size(); ++i)
ans += wt[i] * ::Rf_dgamma(y[i], invdisp, mu[i] * disp, true);
return -2. * ans + 2.;
}
double computeBinWidth(const MatrixXd& positions) {
// assumes first col of positions corresponds to dominant eigenvect
ArrayXd firstCol = positions.col(0).array();
firstCol -= firstCol.mean();
double SSE = firstCol.matrix().squaredNorm();
double variance = SSE / firstCol.size();
double std = sqrt(variance);
double targetBinsPerStd = (MAX_HASH_VALUE - HASH_VALUE_OFFSET) / TARGET_HASH_SPREAD_STDS;
return std / targetBinsPerStd;
}
//@{
double binomialDist::aic (const ArrayXd& y, const ArrayXd& n, const ArrayXd& mu,
const ArrayXd& wt, double dev) const {
ArrayXd m((n > 1).any() ? n : wt);
ArrayXd yy((m * y).unaryExpr(Round<double>()));
m = m.unaryExpr(Round<double>());
double ans(0.);
for (int i=0; i < mu.size(); ++i)
ans += (m[i] <= 0. ? 0. : wt[i]/m[i]) * ::Rf_dbinom(yy[i], m[i], mu[i], true);
return (-2. * ans);
}
ArrayXd GoSUM::CModelVariables::expandNTuple(const ArrayXd &X) const
{
if ( X.size()!=mvs.size() ) throw "GoSUM::CModelVariables::expand error: wrong X size";
int i,j,k,N=int(mvs.size()),eN=expandedSize(),exsize;
ArrayXd eX=ArrayXd::Zero(eN);
for ( i=j=0; i<N; i++,j+=exsize )
{ exsize=mvs[i].expandedSize();
if ( exsize==1 ) { eX(j)=X(i); }
else { for ( k=0; k<exsize; k++ ) if (k==X(i)) { eX(j+k) = 1.; break; } } }
return eX;
}
void merPredD::updateXwts(const ArrayXd& sqrtXwt) {
if (d_Xwts.size() != sqrtXwt.size())
throw invalid_argument("updateXwts: dimension mismatch");
std::copy(sqrtXwt.data(), sqrtXwt.data() + sqrtXwt.size(), d_Xwts.data());
if (sqrtXwt.size() == d_V.rows()) { // W is diagonal
d_V = d_Xwts.asDiagonal() * d_X;
for (int j = 0; j < d_N; ++j)
for (MSpMatrixd::InnerIterator Utj(d_Ut, j), Ztj(d_Zt, j);
Utj && Ztj; ++Utj, ++Ztj)
Utj.valueRef() = Ztj.value() * d_Xwts.data()[j];
} else {
SpMatrixd W(d_V.rows(), sqrtXwt.size());
const double *pt = sqrtXwt.data();
W.reserve(sqrtXwt.size());
for (Index j = 0; j < W.cols(); ++j, ++pt) {
W.startVec(j);
W.insertBack(j % d_V.rows(), j) = *pt;
}
W.finalize();
d_V = W * d_X;
SpMatrixd Ut(d_Zt * W.adjoint());
if (Ut.cols() != d_Ut.cols())
throw std::runtime_error("Size mismatch in updateXwts");
// More complex code to handle the pruning of zeros
MVec(d_Ut.valuePtr(), d_Ut.nonZeros()).setZero();
for (int j = 0; j < d_Ut.outerSize(); ++j) {
MSpMatrixd::InnerIterator lhsIt(d_Ut, j);
for (SpMatrixd::InnerIterator rhsIt(Ut, j); rhsIt; ++rhsIt, ++lhsIt) {
Index k(rhsIt.index());
while (lhsIt && lhsIt.index() != k) ++lhsIt;
if (lhsIt.index() != k)
throw std::runtime_error("Pattern mismatch in updateXwts");
lhsIt.valueRef() = rhsIt.value();
}
}
}
d_VtV.setZero().selfadjointView<Eigen::Upper>().rankUpdate(d_V.adjoint());
updateL();
}
double glmDist::aic(const ArrayXd& y, const ArrayXd& n, const ArrayXd& mu,
const ArrayXd& wt, double dev) const {
int nn = mu.size();
double ans =
::Rf_asReal(::Rf_eval(::Rf_lang6(as<SEXP>(d_aic),
as<SEXP>(NumericVector(y.data(), y.data() + nn)),
as<SEXP>(NumericVector(n.data(), n.data() + nn)),
as<SEXP>(NumericVector(mu.data(), mu.data() + nn)),
as<SEXP>(NumericVector(wt.data(), wt.data() + nn)),
PROTECT(::Rf_ScalarReal(dev))), d_rho));
UNPROTECT(1);
return ans;
}
int gesdd(MatrixXd& A, ArrayXd& S, MatrixXd& Vt) {
int info, mone = -1, m = A.rows(), n = A.cols();
std::vector<int> iwork(8 * n);
double wrk;
if (m < n || S.size() != n || Vt.rows() != n || Vt.cols() != n)
throw std::invalid_argument("dimension mismatch in gesvd");
F77_CALL(dgesdd)("O", &m, &n, A.data(), &m, S.data(), A.data(),
&m, Vt.data(), &n, &wrk, &mone, &iwork[0], &info);
int lwork(wrk);
std::vector<double> work(lwork);
F77_CALL(dgesdd)("O", &m, &n, A.data(), &m, S.data(), A.data(),
&m, Vt.data(), &n, &work[0], &lwork, &iwork[0], &info);
return info;
}
const ArrayXd binomialDist::devResid(const ArrayXd& y, const ArrayXd& mu, const ArrayXd& wt) const {
int debug=0;
if (debug) {
for (int i=0; i < mu.size(); ++i) {
double r = 2. * wt[i] * (Y_log_Y(y[i], mu[i]) + Y_log_Y(1. - y[i], 1. - mu[i]));
if (r!=r) {
// attempt to detect `nan` (needs cross-platform testing, but should compile
// everywhere whether or not it actually works)
Rcpp::Rcout << "(bD) " << "nan @ pos " << i << ": y= " << y[i]
<< "; mu=" << mu[i]
<< "; wt=" << wt[i]
<< "; 1-y=" << 1. - y[i]
<< "; 1-mu=" << 1. - mu[i]
<< "; ylogy=" << Y_log_Y(y[i], mu[i])
<< "; cylogy=" << Y_log_Y(1.-y[i], 1.-mu[i])
<< std::endl;
}
}
}
return 2. * wt * (Y_log_Y(y, mu) + Y_log_Y(1. - y, 1. - mu));
}
void NestedSampler::setLogWeightOfPosteriorSample(ArrayXd newLogWeightOfPosteriorSample)
{
int Nsamples = newLogWeightOfPosteriorSample.size();
logWeightOfPosteriorSample.resize(Nsamples);
logWeightOfPosteriorSample = newLogWeightOfPosteriorSample;
}
//@{
double GaussianDist::aic (const ArrayXd& y, const ArrayXd& n, const ArrayXd& mu,
const ArrayXd& wt, double dev) const {
double nn(mu.size());
return nn * (std::log(2. * M_PI * dev/nn) + 1.) + 2. - wt.log().sum();
}
const ArrayXd GaussianDist::variance(const ArrayXd& mu) const {return ArrayXd::Ones(mu.size());}
//@{
double PoissonDist::aic (const ArrayXd& y, const ArrayXd& n, const ArrayXd& mu,
const ArrayXd& wt, double dev) const {
double ans(0.);
for (int i = 0; i < mu.size(); ++i) ans += ::Rf_dpois(y[i], mu[i], true) * wt[i];
return (-2. * ans);
}
const ArrayXd identityLink::muEta( const ArrayXd& eta) const {return ArrayXd::Ones(eta.size());}
const ArrayXd glmLink::linkFun(const ArrayXd& mu) const {
return as<ArrayXd>(::Rf_eval(::Rf_lang2(as<SEXP>(d_linkFun),
as<SEXP>(Rcpp::NumericVector(mu.data(),
mu.data() + mu.size()))
), d_rho));
}
const ArrayXd glmLink::muEta(const ArrayXd &eta) const {
return as<ArrayXd>(::Rf_eval(::Rf_lang2(as<SEXP>(d_muEta),
as<SEXP>(Rcpp::NumericVector(eta.data(),
eta.data() + eta.size()))
), d_rho));
}
const ArrayXd glmDist::variance(const ArrayXd &mu) const {
return as<ArrayXd>(::Rf_eval(::Rf_lang2(as<SEXP>(d_variance),
as<SEXP>(Rcpp::NumericVector(mu.data(),
mu.data() + mu.size()))
), d_rho));
}