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A library for working with phylogenetic and population genetic data.
v0.27.0 |
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A library for working with phylogenetic and population genetic data.
v0.27.0 |
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#include "genesis/utils/containers/matrix.hpp"#include "genesis/utils/math/statistics.hpp"#include <cmath>#include <limits>#include <vector>Go to the source code of this file.
Namespaces | |
| genesis | |
| Container namespace for all symbols of genesis in order to keep them separate when used as a library. | |
| genesis::utils | |
Functions | |
| Matrix< double > | correlation_matrix (Matrix< double > const &data) |
Calculate the correlation Matrix of a given data Matrix. More... | |
| Matrix< double > | covariance_matrix (Matrix< double > const &data) |
Calculate the covariance Matrix of a given data Matrix. More... | |
| std::vector< size_t > | filter_constant_columns (Matrix< double > &data, double epsilon=1e-5) |
Filter out columns that have nearly constant values, measured using an epsilon. More... | |
| template<typename T = double, typename A = double, typename B = double> | |
| Matrix< T > | matrix_addition (Matrix< A > const &a, Matrix< B > const &b) |
| Calculate the element-wise sum of two Matrices. More... | |
| template<typename T = double, typename A = double, typename B = double> | |
| Matrix< T > | matrix_addition (Matrix< A > const &matrix, B const &scalar) |
| Calculate the element-wise sum of a Matrix and a scalar. More... | |
| template<typename T > | |
| std::vector< MinMaxPair< T > > | matrix_col_minmax (Matrix< T > const &data, bool ignore_non_finite_values=true) |
| Calculate the column-wise min and max values of a Matrix. More... | |
| template<typename T > | |
| std::vector< T > | matrix_col_sums (Matrix< T > const &data, bool ignore_non_finite_values=true) |
| Calculate the sum of each column and return the result as a vector. More... | |
| template<typename T > | |
| MinMaxPair< T > | matrix_minmax (Matrix< T > const &data, bool ignore_non_finite_values=true) |
| Calculate the min and max values of a Matrix. More... | |
| template<typename T = double, typename A = double, typename B = double> | |
| Matrix< T > | matrix_multiplication (Matrix< A > const &a, Matrix< B > const &b) |
| Calculate the product of two Matrices. More... | |
| template<typename T = double, typename A = double, typename B = double> | |
| std::vector< T > | matrix_multiplication (Matrix< A > const &a, std::vector< B > const &b) |
Calculate the product of a Matrices a with a vector b, as if the vector was a Matrix with only one column. More... | |
| template<typename T = double, typename A = double, typename B = double> | |
| Matrix< T > | matrix_multiplication (Matrix< A > const &matrix, B const &scalar) |
| Calculate the element-wise multiplication of a Matrix and a scalar. More... | |
| template<typename T = double, typename A = double, typename B = double> | |
| std::vector< T > | matrix_multiplication (std::vector< A > const &a, Matrix< B > const &b) |
Calculate the product of a vector a with a Matrices b, as if the vector was a Matrix with only one row. More... | |
| template<typename T > | |
| std::vector< MinMaxPair< T > > | matrix_row_minmax (Matrix< T > const &data, bool ignore_non_finite_values=true) |
| Calculate the row-wise min and max values of a Matrix. More... | |
| template<typename T > | |
| std::vector< T > | matrix_row_sums (Matrix< T > const &data, bool ignore_non_finite_values=true) |
| Calculate the sum of each row and return the result as a vector. More... | |
| template<typename T > | |
| Matrix< T > | matrix_sort_by_col_sum_symmetric (Matrix< T > const &data) |
| Sort rows and columns of a Matrix by the sum or the columns. More... | |
| template<typename T > | |
| Matrix< T > | matrix_sort_by_row_sum_symmetric (Matrix< T > const &data) |
| Sort rows and columns of a Matrix by the sum or the rows. More... | |
| template<typename T > | |
| Matrix< T > | matrix_sort_diagonal_symmetric (Matrix< T > const &data) |
| Sort a Matrix so that the highest entries are on the diagonal. More... | |
| template<typename T = double, typename A = double, typename B = double> | |
| Matrix< T > | matrix_subtraction (Matrix< A > const &a, Matrix< B > const &b) |
| Calculate the element-wise difference of two Matrices. More... | |
| template<typename T > | |
| T | matrix_sum (Matrix< T > const &data, bool ignore_non_finite_values=true) |
| Calculate the sum of all elements in a Matrix. More... | |
| std::vector< MinMaxPair< double > > | normalize_cols (Matrix< double > &data) |
Normalize the columns of a Matrix so that all values are in the range [ 0.0, 1.0 ]. More... | |
| std::vector< MinMaxPair< double > > | normalize_rows (Matrix< double > &data) |
Normalize the rows of a Matrix so that all values are in the range [ 0.0, 1.0 ]. More... | |
| std::vector< MeanStddevPair > | standardize_cols (Matrix< double > &data, bool scale_means=true, bool scale_std=true) |
| Standardize the columns of a Matrix by subtracting the mean and scaling to unit variance. More... | |
| std::vector< MeanStddevPair > | standardize_rows (Matrix< double > &data, bool scale_means=true, bool scale_std=true) |
| Standardize the rows of a Matrix by subtracting the mean and scaling to unit variance. More... | |
| Matrix< double > | sums_of_squares_and_cross_products_matrix (Matrix< double > const &data) |
| Calculate the Sums of Squares and Cross Products Matrix (SSCP Matrix). More... | |
1.8.17