sequence/functions/entropy.cpp File Reference

#include "genesis/sequence/functions/entropy.hpp"
#include "genesis/sequence/counts.hpp"
#include "genesis/sequence/sequence_set.hpp"
#include "genesis/sequence/sequence.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::sequence

Functions
double	absolute_entropy (SiteCounts const &counts, SiteEntropyOptions per_site_options=SiteEntropyOptions::kDefault)
	Return the sum of all site entropies. More...
double	absolute_information (SiteCounts const &counts, bool use_small_sample_correction=false, SiteEntropyOptions per_site_options=SiteEntropyOptions::kDefault)
	Calculate the information content across all sites of a SiteCounts object. More...
double	average_entropy (SiteCounts const &counts, bool only_determined_sites=false, SiteEntropyOptions per_site_options=SiteEntropyOptions::kDefault)
	Return the average sum of all site entropies. More...
double	average_information (SiteCounts const &counts, bool only_determined_sites=false, bool use_small_sample_correction=false, SiteEntropyOptions per_site_options=SiteEntropyOptions::kDefault)
	Calculate the information content across all sites of a SiteCounts object. More...
double	site_entropy (SiteCounts const &counts, size_t site_index, SiteEntropyOptions options=SiteEntropyOptions::kDefault)
	Calculate the entropy at one site of a SiteCounts object. More...
double	site_information (SiteCounts const &counts, size_t site_index, bool use_small_sample_correction=false, SiteEntropyOptions options=SiteEntropyOptions::kDefault)
	Calculate the information content at one site of a SiteCounts object. More...