A toolkit for working with phylogenetic data.
v0.24.0
math/matrix.cpp File Reference
#include "genesis/utils/math/matrix.hpp"
#include "genesis/utils/math/common.hpp"
#include "genesis/utils/math/statistics.hpp"
#include <algorithm>
#include <cassert>
#include <cmath>
#include <stdexcept>

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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...
 
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...