Flock Class Reference

A Flock is a group of Geese. More...

#include <flock-bones.hpp>

Public Member Functions
	Flock ()
	~Flock ()
size_t	add_data (std::vector< std::vector< size_t > > &annotations, std::vector< size_t > &geneid, std::vector< int > &parent, std::vector< bool > &duplication)
	Add a tree to the flock. More...
void	set_seed (const size_t &s)
	Set the seed of the model. More...
void	init (size_t bar_width=BARRY_PROGRESS_BAR_WIDTH)
PhyloCounters *	get_counters ()
PhyloSupport *	get_support_fun ()
std::vector< double > *	get_stats_support ()
std::vector< std::vector< double > > *	get_stats_target ()
PhyloModel *	get_model ()
double	likelihood_joint (const std::vector< double > &par, bool as_log=false, bool use_reduced_sequence=true, size_t ncores=1u)
	Returns the joint likelihood of the model. More...
Geese *	operator() (size_t i, bool check_bounds=true)
	Access the i-th geese element. More...
Information about the model
size_t	nfuns () const noexcept
size_t	ntrees () const noexcept
std::vector< size_t >	nnodes () const noexcept
std::vector< size_t >	nleafs () const noexcept
size_t	nterms () const
size_t	support_size () const noexcept
std::vector< std::string >	colnames () const
size_t	parse_polytomies (bool verb=true, std::vector< size_t > *dist=nullptr) const noexcept
	Check polytomies and return the largest. More...
void	print () const

Public Attributes
std::vector< Geese >	dat
size_t	nfunctions = 0u
bool	initialized = false
std::mt19937	rengine
PhyloModel	model = PhyloModel()

Detailed Description

A Flock is a group of Geese.

This object buils a model with multiple trees (Geese objects), with all of these using the same PhyloModel object. Available counters (terms) can be found in counter-phylo.

Definition at line 14 of file flock-bones.hpp.

Constructor & Destructor Documentation

Flock()

Flock::Flock ( )

inline

Definition at line 25 of file flock-bones.hpp.

~Flock()

Flock::~Flock ( )

inline

Definition at line 26 of file flock-bones.hpp.

Member Function Documentation

add_data()

size_t Flock::add_data ( std::vector< std::vector< size_t > > &  annotations, std::vector< size_t > &  geneid, std::vector< int > &  parent, std::vector< bool > &  duplication  )

inline

Add a tree to the flock.

Parameters

annotations	see Geese::Geese.
geneid	see Geese.
parent	see Geese.
duplication	see Geese.

Returns

size_t The number of tree in the model (starting from zero).

Definition at line 6 of file flock-meat.hpp.

colnames()

std::vector< std::string > Flock::colnames ( ) const

inline

Definition at line 246 of file flock-meat.hpp.

get_counters()

PhyloCounters * Flock::get_counters ( )

inline

Definition at line 100 of file flock-meat.hpp.

get_model()

PhyloModel * Flock::get_model ( )

inline

Definition at line 131 of file flock-meat.hpp.

get_stats_support()

std::vector< double > * Flock::get_stats_support ( )

inline

Definition at line 117 of file flock-meat.hpp.

get_stats_target()

std::vector< std::vector< double > > * Flock::get_stats_target ( )

inline

Definition at line 124 of file flock-meat.hpp.

get_support_fun()

PhyloSupport * Flock::get_support_fun ( )

inline

Definition at line 110 of file flock-meat.hpp.

init()

void Flock::init ( size_t  bar_width = BARRY_PROGRESS_BAR_WIDTH )

inline

Definition at line 49 of file flock-meat.hpp.

likelihood_joint()

double Flock::likelihood_joint ( const std::vector< double > &  par, bool  as_log = false, bool  use_reduced_sequence = true, size_t  ncores = 1u  )

inline

Returns the joint likelihood of the model.

Parameters

par	Vector of model parameters.
as_log	When true it will return the value as log.
use_reduced_sequence	When true (default) will compute the likelihood using the reduced sequence, which is faster.

Returns

double

Definition at line 138 of file flock-meat.hpp.

nfuns()

size_t Flock::nfuns ( ) const

inlinenoexcept

Definition at line 189 of file flock-meat.hpp.

nleafs()

std::vector< size_t > Flock::nleafs ( ) const

inlinenoexcept

Definition at line 217 of file flock-meat.hpp.

nnodes()

std::vector< size_t > Flock::nnodes ( ) const

inlinenoexcept

Definition at line 203 of file flock-meat.hpp.

nterms()

size_t Flock::nterms ( ) const

inline

Definition at line 231 of file flock-meat.hpp.

ntrees()

size_t Flock::ntrees ( ) const

inlinenoexcept

Definition at line 196 of file flock-meat.hpp.

operator()()

Geese * Flock::operator() ( size_t  i, bool  check_bounds = true  )

inline

Access the i-th geese element.

Parameters

i	Element to access
check_bounds	When true, it will check bounds.

Returns

Geese*

Definition at line 324 of file flock-meat.hpp.

parse_polytomies()

size_t Flock::parse_polytomies ( bool  verb = true, std::vector< size_t > *  dist = nullptr  ) const

inlinenoexcept

Check polytomies and return the largest.

Definition at line 253 of file flock-meat.hpp.

print()

void Flock::print ( ) const

inline

Definition at line 280 of file flock-meat.hpp.

set_seed()

void Flock::set_seed ( const size_t &  s )

inline

Set the seed of the model.

Parameters

s	Passed to the rengine.seed() member object.

Definition at line 42 of file flock-meat.hpp.

support_size()

size_t Flock::support_size ( ) const

inlinenoexcept

Definition at line 239 of file flock-meat.hpp.

Member Data Documentation

dat

std::vector< Geese > Flock::dat

Definition at line 17 of file flock-bones.hpp.

initialized

bool Flock::initialized = false

Definition at line 19 of file flock-bones.hpp.

model

PhyloModel Flock::model = PhyloModel()

Definition at line 23 of file flock-bones.hpp.

nfunctions

size_t Flock::nfunctions = 0u

Definition at line 18 of file flock-bones.hpp.

rengine

std::mt19937 Flock::rengine

Definition at line 22 of file flock-bones.hpp.

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The documentation for this class was generated from the following files:

• include/barry/models/geese/flock-bones.hpp
• include/barry/models/geese/flock-meat.hpp