diff options
Diffstat (limited to 'src/mathfunc.h')
| -rw-r--r-- | src/mathfunc.h | 44 |
1 files changed, 27 insertions, 17 deletions
diff --git a/src/mathfunc.h b/src/mathfunc.h index 6e20b37..8258c22 100644 --- a/src/mathfunc.h +++ b/src/mathfunc.h @@ -1,25 +1,27 @@ /* - Genome-wide Efficient Mixed Model Association (GEMMA) - Copyright (C) 2011-2017, Xiang Zhou + Genome-wide Efficient Mixed Model Association (GEMMA) + Copyright © 2011-2017, Xiang Zhou + Copyright © 2017, Peter Carbonetto + Copyright © 2017, Pjotr Prins - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. - You should have received a copy of the GNU General Public License - along with this program. If not, see <http://www.gnu.org/licenses/>. + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. */ #ifndef __MATHFUNC_H__ #define __MATHFUNC_H__ -#include "Eigen/Dense" +// #include "Eigen/Dense" #include "gsl/gsl_matrix.h" #include "gsl/gsl_vector.h" @@ -27,9 +29,16 @@ #define EIGEN_MINVALUE 1e-10 using namespace std; -using namespace Eigen; + +inline bool is_nan(double f) { + return (std::isnan(f)); +} bool has_nan(const vector<double> v); +bool has_nan(const gsl_vector *v); +bool has_inf(const gsl_vector *v); +bool has_nan(const gsl_matrix *m); +bool has_inf(const gsl_matrix *m); double VectorVar(const gsl_vector *v); void CenterMatrix(gsl_matrix *G); @@ -38,11 +47,12 @@ void CenterMatrix(gsl_matrix *G, const gsl_matrix *W); void StandardizeMatrix(gsl_matrix *G); double ScaleMatrix(gsl_matrix *G); bool has_negative_values_but_one(const gsl_vector *v); -uint count_small_values(const gsl_vector *v, double min); +uint count_abs_small_values(const gsl_vector *v, double min); bool isMatrixPositiveDefinite(const gsl_matrix *G); bool isMatrixIllConditioned(const gsl_vector *eigenvalues, double max_ratio=CONDITIONED_MAXRATIO); bool isMatrixSymmetric(const gsl_matrix *G); gsl_vector *getEigenValues(const gsl_matrix *G); +double sum(const double *m, size_t rows, size_t cols); double SumVector(const gsl_vector *v); double CenterVector(gsl_vector *y); void CenterVector(gsl_vector *y, const gsl_matrix *W); @@ -56,7 +66,7 @@ void KroneckerSym(const gsl_matrix *K, const gsl_matrix *V, gsl_matrix *H); double UcharToDouble02(const unsigned char c); unsigned char Double02ToUchar(const double dosage); -void uchar_matrix_get_row(const vector<vector<unsigned char>> &X, - const size_t i_row, VectorXd &x_row); +// void uchar_matrix_get_row(const vector<vector<unsigned char>> &X, +// const size_t i_row, Eigen::VectorXd &x_row); #endif |