sequence/functions/entropy.hpp File Reference

#include <cstddef>
#include <type_traits>
#include <string>

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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

Enumerations
enum	SiteEntropyOptions : unsigned char { kDefault = 0, kIncludeGaps = 1, kWeighted = 2, kNormalized = 4 }
	Option flags to refine the calculation of site_entropy(). More...

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...
bool	operator& (SiteEntropyOptions lhs, SiteEntropyOptions rhs)
	And-operator to check whether a SiteEntropyOptions is set. More...
SiteEntropyOptions	operator| (SiteEntropyOptions lhs, SiteEntropyOptions rhs)
	Or-operator to combine two SiteEntropyOptionss. More...
SiteEntropyOptions &	operator|= (SiteEntropyOptions &lhs, SiteEntropyOptions rhs)
	Or-assignment-operator to combine two SiteEntropyOptionss. 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...