A library for working with phylogenetic data.
v0.25.0
structure.hpp File Reference
#include "genesis/population/functions/variant.hpp"
#include "genesis/population/variant.hpp"
#include "genesis/utils/containers/matrix.hpp"
#include "genesis/utils/containers/transform_iterator.hpp"
#include <algorithm>
#include <cassert>
#include <cmath>
#include <stdexcept>
#include <string>
#include <utility>
#include <vector>

Go to the source code of this file.

Classes

struct  FstAN
 Helper struct for the a_1, a_2, n_1, and n_2 values needed for f_st_asymptotically_unbiased(). More...
 

Namespaces

 genesis
 Container namespace for all symbols of genesis in order to keep them separate when used as a library.
 
 genesis::population
 

Functions

template<class ForwardIterator >
utils::Matrix< double > f_st_asymptotically_unbiased (ForwardIterator begin, ForwardIterator end)
 Compute the asymptotically unbiased F_ST estimator of Karlsson et al, for all pairs of ranges of BaseCountss. More...
 
template<class ForwardIterator1 , class ForwardIterator2 >
double f_st_asymptotically_unbiased (ForwardIterator1 p1_begin, ForwardIterator1 p1_end, ForwardIterator2 p2_begin, ForwardIterator2 p2_end)
 Compute the asymptotically unbiased F_ST estimator of Karlsson et al. More...
 
FstAN f_st_asymptotically_unbiased_a1n1a2n2 (BaseCounts const &p1, BaseCounts const &p2)
 Compute the a and n values needed for the asymptotically unbiased F_ST estimator of Karlsson et al. More...
 
std::pair< double, double > f_st_asymptotically_unbiased_nkdk (FstAN const &fstan)
 Compute the N_k and D_k values needed for the asymptotically unbiased F_ST estimator of Karlsson et al. More...
 
template<class ForwardIterator >
utils::Matrix< double > f_st_conventional_pool (size_t number_of_samples, size_t poolsizes, ForwardIterator begin, ForwardIterator end)
 Compute the conventional F_ST statistic for pool-sequenced data, following Kofler et al, for all pairs of ranges of BaseCountss. More...
 
template<class ForwardIterator1 , class ForwardIterator2 >
double f_st_conventional_pool (size_t p1_poolsize, size_t p2_poolsize, ForwardIterator1 p1_begin, ForwardIterator1 p1_end, ForwardIterator2 p2_begin, ForwardIterator2 p2_end)
 Compute the conventional F_ST statistic for pool-sequenced data, following Kofler et al, for two ranges of BaseCountss. More...
 
template<class ForwardIterator >
utils::Matrix< double > f_st_conventional_pool (std::vector< size_t > const &poolsizes, ForwardIterator begin, ForwardIterator end)
 Compute the conventional F_ST statistic for pool-sequenced data, following Kofler et al, for all pairs of ranges of BaseCountss. More...
 
std::tuple< double, double, double > f_st_conventional_pool_pi_snp (BaseCounts const &p1, BaseCounts const &p2)
 Compute the SNP-based Theta Pi values used in f_st_conventional_pool() More...
 
bool operator== (FstAN const &f1, FstAN const &f2)
 Comparison operator equals for FstAN structs. More...