A toolkit for working with phylogenetic data.
v0.18.0
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common.cpp File Reference
#include "genesis/utils/core/algorithm.hpp"
#include "genesis/utils/math/common.hpp"
#include "genesis/utils/core/logging.hpp"
#include <algorithm>
#include <cassert>
#include <cmath>

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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

double fisher_transformation (double correlation_coefficient)
 Apply Fisher z-transformation to a correlation coefficient. More...
 
std::vector< double > fisher_transformation (std::vector< double > const &correlation_coefficients)
 Apply Fisher z-transformation to a vector of correlation coefficients. More...
 
MeanStddevPair mean_stddev (std::vector< double > const &vec, double epsilon=-1.0)
 Calcualte the mean and standard deviation of a vector of double. More...
 
double median (std::vector< double > const &vec, size_t l, size_t r)
 Local helper function to get the median in between a range. More...
 
double median (std::vector< double > const &vec)
 Calculate the median value of a vector of double. More...
 
double pearson_correlation_coefficient (std::vector< double > const &vec_a, std::vector< double > const &vec_b)
 Calculate the Pearson Correlation Coefficient between the entries of two vectors. More...
 
Quartiles quartiles (std::vector< double > const &vec)
 Calculate the Quartiles of a vector of double. More...
 
std::vector< size_t > ranking_dense (std::vector< double > const &vec)
 Return the ranking of the given values, using Dense ranking ("1223" ranking). More...
 
std::vector< double > ranking_fractional (std::vector< double > const &vec)
 Return the ranking of the given values, using Fractional ranking ("1 2.5 2.5 4" ranking). More...
 
std::vector< size_t > ranking_modified (std::vector< double > const &vec)
 Return the ranking of the given values, using Modified competition ranking ("1334" ranking). More...
 
std::vector< size_t > ranking_ordinal (std::vector< double > const &vec)
 Return the ranking of the given values, using Ordinal ranking ("1234" ranking). More...
 
std::vector< size_t > ranking_standard (std::vector< double > const &vec)
 Return the ranking of the given values, using Standard competition ranking ("1224" ranking). More...
 
double spearmans_rank_correlation_coefficient (std::vector< double > const &vec_a, std::vector< double > const &vec_b)
 Calculate Spearman's Rank Correlation Coefficient between the entries of two vectors. More...