typename boost::math::tools::promote_args<T_y, T_covar, T_w>::type
multi_gp_cholesky_log(const Eigen::Matrix
<T_y, Eigen::Dynamic, Eigen::Dynamic>& y,
const Eigen::Matrix
<T_covar, Eigen::Dynamic, Eigen::Dynamic>& L,
const Eigen::Matrix<T_w, Eigen::Dynamic, 1>& w) {
static const char* function("multi_gp_cholesky_log");
typedef
typename boost::math::tools::promote_args<T_y, T_covar, T_w>::type T_lp;
T_lp lp(0.0);
check_size_match(function,
"Size of random variable (rows y)", y.rows(),
"Size of kernel scales (w)", w.size());
check_size_match(function,
"Size of random variable", y.cols(),
"rows of covariance parameter", L.rows());
check_finite(function, "Kernel scales", w);
check_positive(function, "Kernel scales", w);
check_finite(function, "Random variable", y);
if (y.rows() == 0)
return lp;
if (include_summand<propto>::value) {
lp += NEG_LOG_SQRT_TWO_PI * y.rows() * y.cols();
}
if (include_summand<propto, T_covar>::value) {
lp -= L.diagonal().array().log().sum() * y.rows();
}
if (include_summand<propto, T_w>::value) {
lp += 0.5 * y.cols() * sum(log(w));
}
if (include_summand<propto, T_y, T_w, T_covar>::value) {
T_lp sum_lp_vec(0.0);
for (int i = 0; i < y.rows(); i++) {
Eigen::Matrix<T_y, Eigen::Dynamic, 1> y_row(y.row(i));
Eigen::Matrix<typename boost::math::tools::promote_args
<T_y, T_covar>::type,
Eigen::Dynamic, 1>
half(mdivide_left_tri_low(L, y_row));
sum_lp_vec += w(i) * dot_self(half);
}
lp -= 0.5*sum_lp_vec;
}
return lp;
}
typename boost::math::tools::promote_args<T_y, T_covar, T_w>::type
multi_gp_log(const Eigen::Matrix<T_y, Eigen::Dynamic, Eigen::Dynamic>& y,
const Eigen::Matrix
<T_covar, Eigen::Dynamic, Eigen::Dynamic>& Sigma,
const Eigen::Matrix<T_w, Eigen::Dynamic, 1>& w) {
static const char* function("multi_gp_log");
typedef typename boost::math::tools::promote_args<T_y, T_covar, T_w>::type
T_lp;
T_lp lp(0.0);
check_positive(function, "Kernel rows", Sigma.rows());
check_finite(function, "Kernel", Sigma);
check_symmetric(function, "Kernel", Sigma);
LDLT_factor<T_covar, Eigen::Dynamic, Eigen::Dynamic> ldlt_Sigma(Sigma);
check_ldlt_factor(function, "LDLT_Factor of Sigma", ldlt_Sigma);
check_size_match(function,
"Size of random variable (rows y)", y.rows(),
"Size of kernel scales (w)", w.size());
check_size_match(function,
"Size of random variable", y.cols(),
"rows of covariance parameter", Sigma.rows());
check_positive_finite(function, "Kernel scales", w);
check_finite(function, "Random variable", y);
if (y.rows() == 0)
return lp;
if (include_summand<propto>::value) {
lp += NEG_LOG_SQRT_TWO_PI * y.rows() * y.cols();
}
if (include_summand<propto, T_covar>::value) {
lp -= 0.5 * log_determinant_ldlt(ldlt_Sigma) * y.rows();
}
if (include_summand<propto, T_w>::value) {
lp += (0.5 * y.cols()) * sum(log(w));
}
if (include_summand<propto, T_y, T_w, T_covar>::value) {
Eigen::Matrix<T_w, Eigen::Dynamic, Eigen::Dynamic>
w_mat(w.asDiagonal());
Eigen::Matrix<T_y, Eigen::Dynamic, Eigen::Dynamic> yT(y.transpose());
lp -= 0.5 * trace_gen_inv_quad_form_ldlt(w_mat, ldlt_Sigma, yT);
}
return lp;
}
inline bool check_corr_matrix(const char* function,
const Eigen::Matrix<T_y,Eigen::Dynamic,Eigen::Dynamic>& y,
const char* name,
T_result* result,
const Policy&) {
if (!check_size_match(function,
y.rows(), "Rows of correlation matrix",
y.cols(), "columns of correlation matrix",
result, Policy()))
return false;
if (!check_positive(function, y.rows(), "rows", result, Policy()))
return false;
if (!check_symmetric(function, y, "y", result, Policy()))
return false;
for (typename Eigen::Matrix<T_y,Eigen::Dynamic,Eigen::Dynamic>::size_type
k = 0; k < y.rows(); ++k) {
if (fabs(y(k,k) - 1.0) > CONSTRAINT_TOLERANCE) {
std::ostringstream message;
message << name << " is not a valid correlation matrix. "
<< name << "(" << k << "," << k
<< ") is %1%, but should be near 1.0";
T_result tmp
= policies::raise_domain_error<T_y>(function,
message.str().c_str(),
y(k,k), Policy());
if (result != 0)
*result = tmp;
return false;
}
}
if (!check_pos_definite(function, y, "y", result, Policy()))
return false;
return true;
}
inline bool check_square(const char* function,
const Eigen::Matrix<T_y,Eigen::Dynamic,Eigen::Dynamic>& y,
const char* name,
T_result* result) {
check_size_match(function,
y.rows(), "Rows of matrix",
y.cols(), "columns of matrix",
result);
return true;
}
inline bool check_matching_sizes(const char* function,
const char* name1,
const T_y1& y1,
const char* name2,
const T_y2& y2) {
check_size_match(function,
"size of ", name1, y1.size(),
"size of ", name2, y2.size());
return true;
}
inline bool check_cov_matrix(const std::string& function,
const std::string& name,
const Eigen::Matrix<T_y,Eigen::Dynamic,Eigen::Dynamic>& y) {
check_size_match(function,
"Rows of covariance matrix", y.rows(),
"columns of covariance matrix", y.cols());
check_positive(function, "rows", y.rows());
check_symmetric(function, name, y);
check_pos_definite(function, name, y);
return true;
}
inline
Eigen::Matrix<typename boost::math::tools::promote_args<T1, T2>::type,
Eigen::Dynamic, 1>
csr_matrix_times_vector(const int& m,
const int& n,
const Eigen::Matrix<T1, Eigen::Dynamic, 1>& w,
const std::vector<int>& v,
const std::vector<int>& u,
const Eigen::Matrix<T2, Eigen::Dynamic, 1>& b) {
typedef typename boost::math::tools::promote_args<T1, T2>::type
result_t;
check_positive("csr_matrix_times_vector", "m", m);
check_positive("csr_matrix_times_vector", "n", n);
check_size_match("csr_matrix_times_vector", "n", n, "b", b.size());
check_size_match("csr_matrix_times_vector", "m", m, "u", u.size() - 1);
check_size_match("csr_matrix_times_vector", "w", w.size(), "v", v.size());
check_size_match("csr_matrix_times_vector", "u/z",
u[m - 1] + csr_u_to_z(u, m - 1) - 1, "v", v.size());
for (unsigned int i = 0; i < v.size(); ++i)
check_range("csr_matrix_times_vector", "v[]", n, v[i]);
Eigen::Matrix<result_t, Eigen::Dynamic, 1> result(m);
result.setZero();
for (int row = 0; row < m; ++row) {
int idx = csr_u_to_z(u, row);
int row_end_in_w = (u[row] - stan::error_index::value) + idx;
int i = 0; // index into dot-product segment entries.
Eigen::Matrix<result_t, Eigen::Dynamic, 1> b_sub(idx);
b_sub.setZero();
for (int nze = u[row] - stan::error_index::value;
nze < row_end_in_w; ++nze, ++i) {
check_range("csr_matrix_times_vector", "j", n, v[nze]);
b_sub.coeffRef(i) = b.coeffRef(v[nze] - stan::error_index::value);
} // loop skipped when z is zero.
Eigen::Matrix<T1, Eigen::Dynamic, 1>
w_sub(w.segment(u[row] - stan::error_index::value, idx));
result.coeffRef(row) = dot_product(w_sub, b_sub);
}
return result;
}
inline bool check_multiplicable(const char* function,
const char* name1,
const T1& y1,
const char* name2,
const T2& y2) {
check_positive_size(function, name1, "rows()", y1.rows());
check_positive_size(function, name2, "cols()", y2.cols());
check_size_match(function,
"Columns of ", name1, y1.cols(),
"Rows of ", name2, y2.rows());
check_positive_size(function, name1, "cols()", y1.cols());
return true;
}
inline bool check_cov_matrix(const char* function,
const Eigen::Matrix<T_y,Eigen::Dynamic,Eigen::Dynamic>& y,
const char* name,
T_result* result) {
check_size_match(function,
y.rows(), "Rows of covariance matrix",
y.cols(), "columns of covariance matrix",
result);
check_positive(function, y.rows(), "rows", result);
check_symmetric(function, y, name, result);
check_pos_definite(function, y, name, result);
return true;
}
typename return_type<T_y, T_loc, T_covar>::type
multi_normal_cholesky_log(const T_y& y,
const T_loc& mu,
const T_covar& L) {
static const char* function("multi_normal_cholesky_log");
typedef typename scalar_type<T_covar>::type T_covar_elem;
typedef typename return_type<T_y, T_loc, T_covar>::type lp_type;
lp_type lp(0.0);
VectorViewMvt<const T_y> y_vec(y);
VectorViewMvt<const T_loc> mu_vec(mu);
size_t size_vec = max_size_mvt(y, mu);
int size_y = y_vec[0].size();
int size_mu = mu_vec[0].size();
if (size_vec > 1) {
int size_y_old = size_y;
int size_y_new;
for (size_t i = 1, size_ = length_mvt(y); i < size_; i++) {
int size_y_new = y_vec[i].size();
check_size_match(function,
"Size of one of the vectors of "
"the random variable", size_y_new,
"Size of another vector of the "
"random variable", size_y_old);
size_y_old = size_y_new;
}
int size_mu_old = size_mu;
int size_mu_new;
for (size_t i = 1, size_ = length_mvt(mu); i < size_; i++) {
int size_mu_new = mu_vec[i].size();
check_size_match(function,
"Size of one of the vectors of "
"the location variable", size_mu_new,
"Size of another vector of the "
"location variable", size_mu_old);
size_mu_old = size_mu_new;
}
(void) size_y_old;
(void) size_y_new;
(void) size_mu_old;
(void) size_mu_new;
}
check_size_match(function,
"Size of random variable", size_y,
"size of location parameter", size_mu);
check_size_match(function,
"Size of random variable", size_y,
"rows of covariance parameter", L.rows());
check_size_match(function,
"Size of random variable", size_y,
"columns of covariance parameter", L.cols());
for (size_t i = 0; i < size_vec; i++) {
check_finite(function, "Location parameter", mu_vec[i]);
check_not_nan(function, "Random variable", y_vec[i]);
}
if (size_y == 0)
return lp;
if (include_summand<propto>::value)
lp += NEG_LOG_SQRT_TWO_PI * size_y * size_vec;
if (include_summand<propto, T_covar_elem>::value)
lp -= L.diagonal().array().log().sum() * size_vec;
if (include_summand<propto, T_y, T_loc, T_covar_elem>::value) {
lp_type sum_lp_vec(0.0);
for (size_t i = 0; i < size_vec; i++) {
Eigen::Matrix<typename return_type<T_y, T_loc>::type,
Eigen::Dynamic, 1> y_minus_mu(size_y);
for (int j = 0; j < size_y; j++)
y_minus_mu(j) = y_vec[i](j)-mu_vec[i](j);
Eigen::Matrix<typename return_type<T_y, T_loc, T_covar>::type,
Eigen::Dynamic, 1>
half(mdivide_left_tri_low(L, y_minus_mu));
// FIXME: this code does not compile. revert after fixing subtract()
// Eigen::Matrix<typename
// boost::math::tools::promote_args<T_covar,
// typename value_type<T_loc>::type,
// typename value_type<T_y>::type>::type>::type,
// Eigen::Dynamic, 1>
// half(mdivide_left_tri_low(L, subtract(y, mu)));
sum_lp_vec += dot_self(half);
}
lp -= 0.5*sum_lp_vec;
}
return lp;
}