double wishpdfln(const MatrixXd &X, const MatrixXd &Sigma, const double df) {
double ldX = logdet(X);
double ldS = logdet(Sigma);
int n = X.rows();
return (0.5*(-df*ldS - Sigma.selfadjointView<Lower>().llt().solve(X).trace() +
(df-n-1.0)*ldX - df*n*log_2) - mvgammaln(0.5*df,n));
}
void EEMS::initialize_diffs( ) {
cerr << "[Diffs::initialize]" << endl;
n_2 = (double)n/2.0; nmin1 = n-1; logn = log(n);
J = MatrixXd::Zero(n,o);
cvec = VectorXd::Zero(o);
cinv = VectorXd::Zero(o);
for ( int i = 0 ; i < n ; i ++ ) {
J(i,graph.get_deme_of_indiv(i)) = 1;
cvec(graph.get_deme_of_indiv(i)) += 1;
}
cinv = pow(cvec.array(),-1.0).matrix(); // cinv is the vector of inverse counts
cmin1 = cvec; cmin1.array() -= 1; // cmin1 is the vector of counts - 1
Diffs = readMatrixXd(params.datapath + ".diffs");
if ((Diffs.rows()!=n)||(Diffs.cols()!=n)) {
cerr << " Error reading dissimilarities matrix " << params.datapath + ".diffs" << endl
<< " Expect a " << n << "x" << n << " matrix of pairwise differences" << endl; exit(1);
}
cerr << " Loaded dissimilarities matrix from " << params.datapath + ".diffs" << endl;
if (!isdistmat(Diffs)) {
cerr << " The dissimilarity matrix is not a full-rank distance matrix" << endl; exit(1);
}
L = MatrixXd::Constant(nmin1,n,-1.0);
L.topRightCorner(nmin1,nmin1).setIdentity();
JtDhatJ = MatrixXd::Zero(o,o);
JtDobsJ = J.transpose()*Diffs*J;
ldLLt = logdet(L*L.transpose());
ldLDLt = logdet(-L*Diffs*L.transpose());
ldDiQ = ldLLt - ldLDLt;
if (cvec.maxCoeff()>1) {
cerr << "[Diffs::initialize] Use this version only if there is at most one sample in every deme" << endl;
exit(1);
}
cerr << "[Diffs::initialize] Done." << endl << endl;
}
// Conversion from a moment Gaussian.
canonical_gaussian_param& operator=(const moment_gaussian_param<T>& mg) {
Eigen::LLT<mat_type>chol(mg.cov);
if (chol.info() != Eigen::Success) {
throw numerical_error(
"canonical_gaussian: Cannot invert the covariance matrix. "
"Are you passing in a non-singular moment Gaussian distribution?"
);
}
mat_type sol_xy = chol.solve(mg.coef);
std::size_t m = mg.head_size();
std::size_t n = mg.tail_size();
resize(m + n);
eta.segment(0, m) = chol.solve(mg.mean);
eta.segment(m, n).noalias() = -sol_xy.transpose() * mg.mean;
lambda.block(0, 0, m, m) = chol.solve(mat_type::Identity(m, m));
lambda.block(0, m, m, n) = -sol_xy;
lambda.block(m, 0, n, m) = -sol_xy.transpose();
lambda.block(m, m, n, n).noalias() = mg.coef.transpose() * sol_xy;
lm = mg.lm - T(0.5) * (eta.segment(0, m).dot(mg.mean)
+ logdet(chol) + m * std::log(two_pi<T>()));
return *this;
}
/** An sample for taylor expansion of logdet(X). */
void taylorSample() {
std::string ans;
char rowChar[5];
int rowTmp = ROW;
sprintf(rowChar, "%d", rowTmp);
std::string row = rowChar;
// Initialize the matrices.
symbolic_matrix_type X("X", ROW, COL);
symbolic_matrix_type X0("X0", ROW, COL);
symbolic_matrix_type Delta("(X-X0)", ROW, COL);
AMD::SymbolicScalarMatlab a2("1/2!");
AMD::SymbolicScalarMatlab a3("1/3!");
SymbolicSMFunc r2(a2,ROW,COL);
SymbolicSMFunc r3(a3,ROW, COL);
// Initialize MatrixMatrixFunction.
SymbolicMMFunc fX(X, false);
SymbolicMMFunc fX0(X0, false);
SymbolicMMFunc fDelta(Delta, true);
// Compute Taylor series iteratively.
SymbolicSMFunc f0 = logdet(fX0);
SymbolicSMFunc f1 = trace(fDelta * transpose(*f0.derivativeFuncVal));
SymbolicSMFunc f2 = trace(fDelta * transpose(*f1.derivativeFuncVal));
SymbolicSMFunc f3 = trace(fDelta * transpose(*f2.derivativeFuncVal));
// Taylor Expansion.
SymbolicSMFunc func = f0 + f1 + r2*f2 + r3*f3;
std::cout<<"The first 4 terms of Taylor Expansion for logdet(X) around X0 is:";
std::cout << std::endl;
std::cout << func.functionVal.getString() << std::endl;
}
// Not a general pseudowishpdfln (because L*Diff*L' at a single locus has rank 1
double pseudowishpdfln(const MatrixXd &X, const MatrixXd &Sigma, const int df) {
int rank = 1;
double ldX = pseudologdet(X,rank);
double ldS = logdet(Sigma);
int n = X.rows();
int q = (df<n) ? df : n;
return (0.5*(-df*ldS - Sigma.selfadjointView<Lower>().llt().solve(X).trace() +
(df-n-1.0)*ldX - df*n*log_2 - df*(n-q)*log_pi) - mvgammaln(0.5*df,q));
}
//----------------------------------------------------------------------
// log posterior if R(i_,j_) is replaced by r. performs work needed
// for slice sampling in draw_R(i,j)
double SepStratSampler::logp_slice_R(double r){
set_R(r);
fill_siginv(false); // false means we need to compute Rinv
const Spd & Siginv(cand_);
double ans = .5 * n_ * logdet(Siginv); // positive .5
ans += -.5 * traceAB(Siginv, sumsq_);
ans += Rpri_->logp(R_);
// skip the jacobian because it only has products of sigma^2's in it
return ans;
}
void CParam::S5_MuSigma(CData &Data, double f_Sigma,double h_Mu) {
vector<Matrix> X = vector<Matrix>(K);
int *Counts = new int[K];
for (int k =0; k < K; k++) {
if (n_z(k+1) > 0) {
X[k] = Matrix(n_z(k+1),n_var_independent); X[k] = 0;
Counts[k] = 0;
}
}
for (int i=1; i<=Y_aug_compact.nrows(); i++){
int k = z_aug(i);
X[k-1].row(++Counts[k-1]) = Y_aug_compact.row(i) - X_bar.column(k).t();
}
SymmetricMatrix SqMatrix;
for (int k=1; k<=K ; k++) {
// propose Sigma_k_q
double f_Sigma_tilde_k = f_Sigma + n_z(k);
double h_k = h_Mu + n_z(k);
SymmetricMatrix Phi_tilde_k = Phi;
ColumnVector mu_tilde_k = mu_bar;
if ( n_z(k) > 0) {
mu_tilde_k = (h_Mu * mu_bar + X_bar.column(k) * n_z(k)) / h_k;
SqMatrix << X[k-1].t() * X[k-1];
Phi_tilde_k += SqMatrix; //can be further optimized
ColumnVector xbar_mubar = X_bar.column(k) - mu_bar;
SqMatrix << (h_Mu*n_z(k)/h_k) * ( xbar_mubar * xbar_mubar.t());
Phi_tilde_k += SqMatrix ;
}
LowerTriangularMatrix LPhi_tilde_k = Cholesky(Phi_tilde_k);
LowerTriangularMatrix LSigma_k_q = rIW_w_pd_check_fn( f_Sigma_tilde_k, LPhi_tilde_k );
// propose mu_k_q
LowerTriangularMatrix LSigma_k_tilde = (1.0/sqrt(h_k)) * LSigma_k_q ;
ColumnVector mu_k_q = rMVN_fn( mu_tilde_k, LSigma_k_tilde ); // Modified
// Gibbs update
Mu.column(k) = mu_k_q ;
LSIGMA[k-1] = LSigma_k_q;
LSIGMA_i[k-1] = LSigma_k_q.i();
SIGMA[k-1] << LSigma_k_q * LSigma_k_q.t();
logdet_and_more(k) = -0.5*n_var* LOG_2_PI + logdet(LSIGMA_i[k-1]);
// S = L * L.t() ; S.i() = (L.i()).t() * L.i() ;
Matrix Sigma_k_inv = LSIGMA_i[k-1].t() * LSIGMA_i[k-1];
for (int i_var=1; i_var<= n_var_independent; i_var++) {
Sigma_k_inv_ll(k,i_var) = Sigma_k_inv(i_var,i_var);
}
}
delete [] Counts;
}
void CParam::init_sigmamu(CData &Data) {
mu_bar = ColumnVector(n_var_independent);
ColumnVector log_obs_mean(n_var), log_obs_sd(n_var) ;
Matrix logD_editpassing(n_sample-Data.n_faulty,n_var) ;
for (int i_sample=1, count = 1; i_sample<=n_sample; i_sample++){
if (Data.is_case(i_sample,0)) {
logD_editpassing.row(count++) = Data.log_D_Observed.row(i_sample);
}
}
for (int i_var=1; i_var<=n_var; i_var++){
ColumnVector temp_col = logD_editpassing.column(i_var) ;
log_obs_mean(i_var) = 1.0/(n_sample-Data.n_faulty)*(temp_col.sum()) ;
ColumnVector temp_mean(n_sample-Data.n_faulty) ; temp_mean = log_obs_mean(i_var) ;
Matrix SumSq = (temp_col-temp_mean).t()*(temp_col-temp_mean) ;
log_obs_sd(i_var) = sqrt( 1.0/(n_sample-Data.n_faulty-1)*SumSq(1,1) ) ;
}
Data.UpdateCompactVector(mu_bar,log_obs_mean);
DiagonalMatrix LSigma_temp(n_var_independent);
for (int i=1; i<= n_var_independent; i++){
LSigma_temp(i) = log_obs_sd(i);
}
DiagonalMatrix LSigma_temp_i = LSigma_temp.i();
LSIGMA = vector<LowerTriangularMatrix>(K);
LSIGMA_i = vector<LowerTriangularMatrix>(K);
SIGMA = vector<SymmetricMatrix>(K);
for (int k=0 ; k<K; k++) {
LSIGMA[k] = LSigma_temp;
LSIGMA_i[k] = LSigma_temp_i;
SIGMA[k] << LSigma_temp * LSigma_temp; //lazy
}
logdet_and_more = ColumnVector(K); logdet_and_more = -0.5*n_var* LOG_2_PI + logdet(LSIGMA_i[0]);
Mu = Matrix((n_var_independent),K); // Note that mu_k is Mu.column(k)
for (int k=1; k<=K; k++){
Mu.column(k) = mu_bar ; // starting value
}
}
void testMatrixMatrixFunc() {
typedef AMD::MatrixMatrixFunc<AMD::SymbolicMatrixMatlab,
AMD::SymbolicScalarMatlab> MMFunc;
typedef AMD::ScalarMatrixFunc<AMD::SymbolicMatrixMatlab,
AMD::SymbolicScalarMatlab> SMFunc;
std::string ans;
AMD::SymbolicMatrixMatlab x("X",3,3);
MMFunc fx(x,true); // a matrix variable
AMD::SymbolicMatrixMatlab y("Y",3,3);
MMFunc fy(y); // a matrix variable
SMFunc func;
ans = "Y'";
// d/dX trace(X*Y)=Y^T
func = trace(fx*fy);
assert(func.derivativeVal.getString()==ans);
// d/dX trace(X^T*Y^T)=Y^T
func = trace(transpose(fx)*transpose(fy));
assert(func.derivativeVal.getString()==ans);
// d/dX trace((X*Y)^T)=Y^T
func = trace(transpose(fx*fy));
assert(func.derivativeVal.getString()==ans);
ans = "Y";
// d/dX trace(X*Y^T) = Y
func = trace(fx*transpose(fy));
assert(func.derivativeVal.getString()==ans);
// d/dX trace(Y*X^T) = Y
func = trace(fy*transpose(fx));
assert(func.derivativeVal.getString()==ans);
ans = "eye(3)";
// d/dX trace(X) = I
func = trace(fx);
assert(func.derivativeVal.getString()==ans);
// d/dX trace(Y+X^T+Y) = I
func = trace(fy+transpose(fx)+fy);
assert(func.derivativeVal.getString()==ans);
func = trace(fy*inv(fx));
ans = "(((-inv(X))*Y)*inv(X))'";
assert(func.derivativeVal.getString()==ans);
assert(func.derivativeVal.getString()==ans);
func = trace(fy-fx);
ans = "(-eye(3))";
assert(func.derivativeVal.getString()==ans);
func = logdet(fx);
ans = "inv(X)'";
assert(func.derivativeVal.getString()==ans);
func = logdet(transpose(fx));
assert(func.derivativeVal.getString()==ans);
func = logdet(fy+fx);
ans = "inv(Y+X)'";
assert(func.derivativeVal.getString()==ans);
func = logdet(fy-fx);
ans = "(-inv(Y-X))'";
assert(func.derivativeVal.getString()==ans);
func = logdet(inv(transpose(fx)));
ans = "(-inv(X)')";
assert(func.derivativeVal.getString()==ans);
std::cout << "d/dX " << func.functionVal.getString()
<< " = " << func.derivativeVal.getString() << std::endl;
}