Rules for phylogenetic modeling. More...

Collaboration diagram for Phylo rules:

Classes
class	DEFMRuleDynData

Functions
	DEFMData::DEFMData ()

	DEFMData::DEFMData (DEFMArray array_, const double covariates_, size_t obs_start_, size_t X_ncol_, size_t X_nrow_, bool column_major_)
	Constructor. More...

double	DEFMData::operator() (size_t i, size_t j) const
	Access to the row (i) colum (j) data. More...

double	DEFMData::at (size_t i, size_t j) const

size_t	DEFMData::ncol () const

size_t	DEFMData::nrow () const

void	DEFMData::print () const

	DEFMData::~DEFMData ()

	DEFMCounterData::DEFMCounterData ()

	DEFMCounterData::DEFMCounterData (const std::vector< size_t > indices_, const std::vector< double > numbers_, const std::vector< bool > logical_, bool is_motif_=true)

size_t	DEFMCounterData::idx (size_t i) const

double	DEFMCounterData::num (size_t i) const

bool	DEFMCounterData::is_true (size_t i) const

	DEFMCounterData::~DEFMCounterData ()

double	DEFMRuleData::num (size_t i) const

size_t	DEFMRuleData::idx (size_t i) const

bool	DEFMRuleData::is_true (size_t i) const

	DEFMRuleData::DEFMRuleData ()

	DEFMRuleData::DEFMRuleData (std::vector< double > numbers_, std::vector< size_t > indices_, std::vector< bool > logical_)

	DEFMRuleData::DEFMRuleData (std::vector< double > numbers_, std::vector< size_t > indices_)

	DEFMRuleDynData::DEFMRuleDynData (const std::vector< double > *counts_, size_t pos_, size_t lb_, size_t ub_)

	DEFMRuleDynData::~DEFMRuleDynData ()

const double	DEFMRuleDynData::operator() () const

void	rule_leafs (PhyloSupport *support)

void	rule_dyn_limit_changes (PhyloSupport *support, size_t pos, size_t lb, size_t ub, size_t duplication=Geese::etype_default)
	Overall functional gains. More...

Variables
DEFMArray *	DEFMData::array

const double *	DEFMData::covariates
	Vector of covariates (complete vector) More...

size_t	DEFMData::obs_start
	Index of the observation in the data. More...

size_t	DEFMData::X_ncol
	Number of columns in the array of covariates. More...

size_t	DEFMData::X_nrow
	Number of rows in the array of covariates. More...

std::vector< size_t >	DEFMData::covar_sort

std::vector< size_t >	DEFMData::covar_used
	Value where the sorting of the covariates is stored. More...

bool	DEFMData::column_major
	Vector indicating which covariates are included in the model. More...

std::vector< size_t >	DEFMCounterData::indices

std::vector< double >	DEFMCounterData::numbers

std::vector< bool >	DEFMCounterData::logical

bool	DEFMCounterData::is_motif
	If false, then is a logit intercept. More...

std::vector< double >	DEFMRuleData::numbers

std::vector< size_t >	DEFMRuleData::indices

std::vector< bool >	DEFMRuleData::logical

bool	DEFMRuleData::init = false

const std::vector< double > *	DEFMRuleDynData::counts

size_t	DEFMRuleDynData::pos

size_t	DEFMRuleDynData::lb

size_t	DEFMRuleDynData::ub

Convenient typedefs for network objects.
typedef barry::Counter< DEFMArray, DEFMCounterData >	DEFMCounter

typedef barry::Counters< DEFMArray, DEFMCounterData >	DEFMCounters

typedef barry::Support< DEFMArray, DEFMCounterData, DEFMRuleData, DEFMRuleDynData >	DEFMSupport

typedef barry::StatsCounter< DEFMArray, DEFMCounterData >	DEFMStatsCounter

typedef barry::Model< DEFMArray, DEFMCounterData, DEFMRuleData, DEFMRuleDynData >	DEFMModel

typedef barry::Rule< DEFMArray, DEFMRuleData >	DEFMRule

typedef barry::Rules< DEFMArray, DEFMRuleData >	DEFMRules

typedef barry::Rule< DEFMArray, DEFMRuleDynData >	DEFMRuleDyn

typedef barry::Rules< DEFMArray, DEFMRuleDynData >	DEFMRulesDyn

Detailed Description

Rules for phylogenetic modeling.

Parameters

rules A pointer to a PhyloRules object (Rules<PhyloArray, PhyloRuleData>).

Typedef Documentation

◆ DEFMCounter

typedef barry::Counter<DEFMArray, DEFMCounterData > DEFMCounter

Definition at line 186 of file defm-types.hpp.

◆ DEFMCounters

typedef barry::Counters<DEFMArray, DEFMCounterData> DEFMCounters

Definition at line 187 of file defm-types.hpp.

◆ DEFMModel

typedef barry::Model<DEFMArray, DEFMCounterData,DEFMRuleData,DEFMRuleDynData> DEFMModel

Definition at line 190 of file defm-types.hpp.

◆ DEFMRule

typedef barry::Rule<DEFMArray, DEFMRuleData> DEFMRule

Definition at line 193 of file defm-types.hpp.

◆ DEFMRuleDyn

typedef barry::Rule<DEFMArray, DEFMRuleDynData> DEFMRuleDyn

Definition at line 195 of file defm-types.hpp.

◆ DEFMRules

typedef barry::Rules<DEFMArray, DEFMRuleData> DEFMRules

Definition at line 194 of file defm-types.hpp.

◆ DEFMRulesDyn

typedef barry::Rules<DEFMArray, DEFMRuleDynData> DEFMRulesDyn

Definition at line 196 of file defm-types.hpp.

◆ DEFMStatsCounter

typedef barry::StatsCounter<DEFMArray, DEFMCounterData> DEFMStatsCounter

Definition at line 189 of file defm-types.hpp.

◆ DEFMSupport

typedef barry::Support<DEFMArray, DEFMCounterData, DEFMRuleData,DEFMRuleDynData> DEFMSupport

Definition at line 188 of file defm-types.hpp.

Function Documentation

◆ at()

double DEFMData::at	(	size_t	i,
		size_t	j
	)		const

◆ DEFMCounterData() [1/2]

DEFMCounterData::DEFMCounterData ( )

inline

Definition at line 74 of file defm-types.hpp.

◆ DEFMCounterData() [2/2]

DEFMCounterData::DEFMCounterData	(	const std::vector< size_t >	indices_,
		const std::vector< double >	numbers_,
		const std::vector< bool >	logical_,
		bool	is_motif_ = `true`
	)

inline

Definition at line 75 of file defm-types.hpp.

◆ DEFMData() [1/2]

DEFMData::DEFMData ( )

inline

Definition at line 28 of file defm-types.hpp.

◆ DEFMData() [2/2]

DEFMData::DEFMData	(	DEFMArray *	array_,
		const double *	covariates_,
		size_t	obs_start_,
		size_t	X_ncol_,
		size_t	X_nrow_,
		bool	column_major_
	)

inline

Constructor.

Parameters

covariates_	Pointer to the attribute data.
obs_start_	Location of the current observation in the covariates vector
X_ncol_	Number of columns (covariates.)

Definition at line 37 of file defm-types.hpp.

◆ DEFMRuleData() [1/3]

DEFMRuleData::DEFMRuleData ( )

inline

Definition at line 104 of file defm-types.hpp.

◆ DEFMRuleData() [2/3]

DEFMRuleData::DEFMRuleData	(	std::vector< double >	numbers_,
		std::vector< size_t >	indices_
	)

inline

Definition at line 112 of file defm-types.hpp.

◆ DEFMRuleData() [3/3]

DEFMRuleData::DEFMRuleData	(	std::vector< double >	numbers_,
		std::vector< size_t >	indices_,
		std::vector< bool >	logical_
	)

inline

Definition at line 106 of file defm-types.hpp.

◆ DEFMRuleDynData()

DEFMRuleDynData::DEFMRuleDynData	(	const std::vector< double > *	counts_,
		size_t	pos_,
		size_t	lb_,
		size_t	ub_
	)

inline

Definition at line 166 of file defm-types.hpp.

◆ idx() [1/2]

size_t DEFMCounterData::idx ( size_t i ) const

inline

Definition at line 83 of file defm-types.hpp.

◆ idx() [2/2]

size_t DEFMRuleData::idx ( size_t i ) const

inline

Definition at line 101 of file defm-types.hpp.

◆ is_true() [1/2]

bool DEFMCounterData::is_true ( size_t i ) const

inline

Definition at line 85 of file defm-types.hpp.

◆ is_true() [2/2]

bool DEFMRuleData::is_true ( size_t i ) const

inline

Definition at line 102 of file defm-types.hpp.

◆ ncol()

size_t DEFMData::ncol ( ) const

inline

Definition at line 130 of file defm-types.hpp.

◆ nrow()

size_t DEFMData::nrow ( ) const

inline

Definition at line 134 of file defm-types.hpp.

◆ num() [1/2]

double DEFMCounterData::num ( size_t i ) const

inline

Definition at line 84 of file defm-types.hpp.

◆ num() [2/2]

double DEFMRuleData::num ( size_t i ) const

inline

Definition at line 100 of file defm-types.hpp.

◆ operator()() [1/2]

const double DEFMRuleDynData::operator() ( ) const

inline

Definition at line 175 of file defm-types.hpp.

◆ operator()() [2/2]

double DEFMData::operator()	(	size_t	i,
		size_t	j
	)		const

inline

Access to the row (i) colum (j) data.

Parameters

i
j

Returns: double

Definition at line 120 of file defm-types.hpp.

◆ print()

void DEFMData::print ( ) const

inline

Definition at line 138 of file defm-types.hpp.

◆ rule_dyn_limit_changes()

void rule_dyn_limit_changes	(	PhyloSupport *	support,
		size_t	pos,
		size_t	lb,
		size_t	ub,
		size_t	duplication = `Geese::etype_default`
	)

inline

Overall functional gains.

Parameters

support	Support of a model.
pos	Position of the focal statistic.
lb	Lower bound
ub	Upper bound

Returns: (void) adds a rule limiting the support of the model.

Definition at line 2087 of file counters.hpp.

◆ rule_leafs()

void rule_leafs ( PhyloSupport * support )

inline

Definition at line 2052 of file counters.hpp.

◆ ~DEFMCounterData()

DEFMCounterData::~DEFMCounterData ( )

inline

Definition at line 87 of file defm-types.hpp.

◆ ~DEFMData()

DEFMData::~DEFMData ( )

inline

Definition at line 60 of file defm-types.hpp.

◆ ~DEFMRuleDynData()

DEFMRuleDynData::~DEFMRuleDynData ( )

inline

Definition at line 173 of file defm-types.hpp.

Variable Documentation

◆ array

DEFMArray* DEFMData::array

Definition at line 19 of file defm-types.hpp.

◆ column_major

bool DEFMData::column_major

Vector indicating which covariates are included in the model.

Definition at line 26 of file defm-types.hpp.

◆ counts

const std::vector< double >* DEFMRuleDynData::counts

Definition at line 161 of file defm-types.hpp.

◆ covar_sort

std::vector< size_t > DEFMData::covar_sort

Definition at line 24 of file defm-types.hpp.

◆ covar_used

std::vector< size_t > DEFMData::covar_used

Value where the sorting of the covariates is stored.

Definition at line 25 of file defm-types.hpp.

◆ covariates

const double* DEFMData::covariates

Vector of covariates (complete vector)

Definition at line 20 of file defm-types.hpp.

◆ indices [1/2]

std::vector< size_t > DEFMCounterData::indices

Definition at line 69 of file defm-types.hpp.

◆ indices [2/2]

std::vector< size_t > DEFMRuleData::indices

Definition at line 95 of file defm-types.hpp.

◆ init

bool DEFMRuleData::init = false

Definition at line 98 of file defm-types.hpp.

◆ is_motif

bool DEFMCounterData::is_motif

If false, then is a logit intercept.

Definition at line 72 of file defm-types.hpp.

◆ lb

size_t DEFMRuleDynData::lb

Definition at line 163 of file defm-types.hpp.

◆ logical [1/2]

std::vector< bool > DEFMCounterData::logical

Definition at line 71 of file defm-types.hpp.

◆ logical [2/2]

std::vector< bool > DEFMRuleData::logical

Definition at line 96 of file defm-types.hpp.

◆ numbers [1/2]

std::vector< double > DEFMCounterData::numbers

Definition at line 70 of file defm-types.hpp.

◆ numbers [2/2]

std::vector< double > DEFMRuleData::numbers

Definition at line 94 of file defm-types.hpp.

◆ obs_start

size_t DEFMData::obs_start

Index of the observation in the data.

Definition at line 21 of file defm-types.hpp.

◆ pos

size_t DEFMRuleDynData::pos

Definition at line 162 of file defm-types.hpp.

◆ ub

size_t DEFMRuleDynData::ub

Definition at line 164 of file defm-types.hpp.

◆ X_ncol

size_t DEFMData::X_ncol

Number of columns in the array of covariates.

Definition at line 22 of file defm-types.hpp.

◆ X_nrow

size_t DEFMData::X_nrow

Number of rows in the array of covariates.

Definition at line 23 of file defm-types.hpp.

Classes

Functions

Variables

Convenient typedefs for network objects.

Detailed Description

Typedef Documentation

◆ DEFMCounter

◆ DEFMCounters

◆ DEFMModel

◆ DEFMRule

◆ DEFMRuleDyn

◆ DEFMRules

◆ DEFMRulesDyn

◆ DEFMStatsCounter

◆ DEFMSupport

Function Documentation

◆ at()

◆ DEFMCounterData() [1/2]

◆ DEFMCounterData() [2/2]

◆ DEFMData() [1/2]

◆ DEFMData() [2/2]

◆ DEFMRuleData() [1/3]

◆ DEFMRuleData() [2/3]

◆ DEFMRuleData() [3/3]

◆ DEFMRuleDynData()

◆ idx() [1/2]

◆ idx() [2/2]

◆ is_true() [1/2]

◆ is_true() [2/2]

◆ ncol()

◆ nrow()

◆ num() [1/2]

◆ num() [2/2]

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ print()

◆ rule_dyn_limit_changes()

◆ rule_leafs()

◆ ~DEFMCounterData()

◆ ~DEFMData()

◆ ~DEFMRuleDynData()

Variable Documentation

◆ array

◆ column_major

◆ counts

◆ covar_sort

◆ covar_used

◆ covariates

◆ indices [1/2]

◆ indices [2/2]

◆ init

◆ is_motif

◆ lb

◆ logical [1/2]

◆ logical [2/2]

◆ numbers [1/2]

◆ numbers [2/2]

◆ obs_start

◆ pos

◆ ub

◆ X_ncol

◆ X_nrow