A container for paired-site likelihoods (likelihoods over the same sites for different models, especially topologies). An instance of this class is, roughly, a list of models, each of them having a name (stored in the modelNames attribute) and a set of site likelihoods (stored in the logLikelihoods attribute). More...

#include <Bpp/Phyl/Legacy/Likelihood/PairedSiteLikelihoods.h>

Collaboration diagram for bpp::PairedSiteLikelihoods:

Public Member Functions
	PairedSiteLikelihoods ()

	PairedSiteLikelihoods (const std::vector< std::vector< double > > &siteLogLikelihoods, const std::vector< std::string > &modelNames=std::vector< std::string >())
	Build a new object from a site likelihoods array. More...

	~PairedSiteLikelihoods ()

void	appendModel (const std::vector< double > &siteLogLikelihoods, const std::string &modelName="")
	Append a model. More...

void	appendModel (const bpp::TreeLikelihoodInterface &treelikelihood)
	Append a model. More...

void	appendModels (const PairedSiteLikelihoods &psl)
	Append models by concatenation. More...

const std::vector< std::vector< double > > &	getLikelihoods () const

const std::vector< std::string > &	getModelNames () const

size_t	getNumberOfModels () const
	Get the number of models in the container. More...

std::size_t	getNumberOfSites () const

void	setName (std::size_t pos, std::string &name)
	Set the name of a model. More...

std::pair< std::vector< std::string >, std::vector< double > >	computeExpectedLikelihoodWeights (int replicates=10000) const
	Compute the Expected Likelihood Weights of the models. More...

Static Public Member Functions
static std::vector< int >	bootstrap (std::size_t length, double scaling=1)
	Draw a nonparametric pseudoreplicate. More...

Private Attributes
std::vector< std::vector< double > >	logLikelihoods_

std::vector< std::string >	modelNames_

Detailed Description

A container for paired-site likelihoods (likelihoods over the same sites for different models, especially topologies). An instance of this class is, roughly, a list of models, each of them having a name (stored in the modelNames attribute) and a set of site likelihoods (stored in the logLikelihoods attribute).

Definition at line 26 of file PairedSiteLikelihoods.h.

Constructor & Destructor Documentation

◆ PairedSiteLikelihoods() [1/2]

PairedSiteLikelihoods::PairedSiteLikelihoods ( )

Definition at line 21 of file PairedSiteLikelihoods.cpp.

◆ PairedSiteLikelihoods() [2/2]

PairedSiteLikelihoods::PairedSiteLikelihoods	(	const std::vector< std::vector< double > > &	siteLogLikelihoods,
		const std::vector< std::string > &	modelNames = `std::vector<std::string>()`
	)

Build a new object from a site likelihoods array.

Parameters

siteLogLikelihoods	An nmodels*nsites array of loglikelihoods.
modelNames	(Optional) The names of the models.

Exceptions

Exception If the number of sites differ between the models, or if the number of names and site loglikelihood records differ.

Definition at line 26 of file PairedSiteLikelihoods.cpp.

References getNumberOfModels(), getNumberOfSites(), and modelNames_.

◆ ~PairedSiteLikelihoods()

bpp::PairedSiteLikelihoods::~PairedSiteLikelihoods ( )

inline

Definition at line 49 of file PairedSiteLikelihoods.h.

Member Function Documentation

◆ appendModel() [1/2]

void PairedSiteLikelihoods::appendModel ( const bpp::TreeLikelihoodInterface & treelikelihood )

Append a model.

Parameters

treelikelihood A TreeLikelihood record.

Exceptions

Exception If the number of sites is not the same as in the container.

Definition at line 64 of file PairedSiteLikelihoods.cpp.

References appendModel(), bpp::TreeLikelihoodInterface::getLogLikelihoodPerSite(), bpp::Tree::getName(), and bpp::TreeLikelihoodInterface::tree().

◆ appendModel() [2/2]

void PairedSiteLikelihoods::appendModel	(	const std::vector< double > &	siteLogLikelihoods,
		const std::string &	modelName = `""`
	)

Append a model.

Parameters

siteLogLikelihoods	The loglikelihoods of the sites under this model.
modelName	The name of the model.

Exceptions

Exception If the number of sites is not the same as in the container.

Definition at line 52 of file PairedSiteLikelihoods.cpp.

References getNumberOfModels(), getNumberOfSites(), logLikelihoods_, and modelNames_.

Referenced by appendModel().

◆ appendModels()

void PairedSiteLikelihoods::appendModels ( const PairedSiteLikelihoods & psl )

Append models by concatenation.

Parameters

psl	the PairedSiteLikelihoods object to append to the caller.

Exceptions

Exception If the number of sites in the two object is not equal.

Definition at line 72 of file PairedSiteLikelihoods.cpp.

References getNumberOfModels(), getNumberOfSites(), logLikelihoods_, and modelNames_.

◆ bootstrap()

std::vector< int > PairedSiteLikelihoods::bootstrap	(	std::size_t	length,
		double	scaling = `1`
	)

static

Draw a nonparametric pseudoreplicate.

Parameters

length	The length of the data.
scaling	The length of the pseudoreplicate, in fraction of the length of the data.

Returns: A vector of the same length as the data, containing the count of each element in the pseudoreplicate.

Definition at line 143 of file PairedSiteLikelihoods.cpp.

Referenced by computeExpectedLikelihoodWeights().

◆ computeExpectedLikelihoodWeights()

pair< vector< string >, vector< double > > PairedSiteLikelihoods::computeExpectedLikelihoodWeights ( int replicates = 10000 ) const

Compute the Expected Likelihood Weights of the models.

The weight of a model is :

$W_m = \frac{1}{B} \sum_{b \in B} \frac{L_m^{(b)}}{\sum L_k^{(b)}} = \frac{1}{B} \sum_{b \in B} \frac{exp(Y^{(b)}_m - Ymax^{(b)})}{\sum exp(Y_k^{(b)} - Y_{max}^{(b)})}$

where $Y_k^{(b)}$ is the loglikelihood of model k for replicate b.

Returns: A pair of vectors containing the names and weights of the models.

Parameters

replicates The number of pseudoreplicates over which the weights are to be averaged.

Definition at line 89 of file PairedSiteLikelihoods.cpp.

References bootstrap(), bpp::exp(), getNumberOfModels(), getNumberOfSites(), logLikelihoods_, and modelNames_.

◆ getLikelihoods()

const std::vector< std::vector< double > > & bpp::PairedSiteLikelihoods::getLikelihoods ( ) const

inline

Returns: The site-likelihoods of all models.

Definition at line 84 of file PairedSiteLikelihoods.h.

References logLikelihoods_.

Referenced by bpp::IOTreepuzzlePairedSiteLikelihoods::writePairedSiteLikelihoods().

◆ getModelNames()

const std::vector< std::string > & bpp::PairedSiteLikelihoods::getModelNames ( ) const

inline

Returns: The model names.

Definition at line 92 of file PairedSiteLikelihoods.h.

References modelNames_.

Referenced by bpp::IOTreepuzzlePairedSiteLikelihoods::writePairedSiteLikelihoods().

◆ getNumberOfModels()

size_t bpp::PairedSiteLikelihoods::getNumberOfModels ( ) const

inline

Get the number of models in the container.

Definition at line 98 of file PairedSiteLikelihoods.h.

References logLikelihoods_.

Referenced by appendModel(), appendModels(), computeExpectedLikelihoodWeights(), PairedSiteLikelihoods(), and bpp::IOTreepuzzlePairedSiteLikelihoods::writePairedSiteLikelihoods().

◆ getNumberOfSites()

std::size_t bpp::PairedSiteLikelihoods::getNumberOfSites ( ) const

inline

Returns: The number of sites for each model.

Exceptions

Exception If the container is empty.

Definition at line 107 of file PairedSiteLikelihoods.h.

References logLikelihoods_.

Referenced by appendModel(), appendModels(), computeExpectedLikelihoodWeights(), PairedSiteLikelihoods(), and bpp::IOTreepuzzlePairedSiteLikelihoods::writePairedSiteLikelihoods().

◆ setName()

void bpp::PairedSiteLikelihoods::setName	(	std::size_t	pos,
		std::string &	name
	)

inline

Set the name of a model.

Parameters

pos	The position of the target model.
name	The new name.

Definition at line 125 of file PairedSiteLikelihoods.h.

References modelNames_.

Member Data Documentation

◆ logLikelihoods_

std::vector<std::vector<double> > bpp::PairedSiteLikelihoods::logLikelihoods_

private

Definition at line 29 of file PairedSiteLikelihoods.h.

Referenced by appendModel(), appendModels(), computeExpectedLikelihoodWeights(), getLikelihoods(), getNumberOfModels(), and getNumberOfSites().

◆ modelNames_

std::vector<std::string> bpp::PairedSiteLikelihoods::modelNames_

private

Definition at line 30 of file PairedSiteLikelihoods.h.

Referenced by appendModel(), appendModels(), computeExpectedLikelihoodWeights(), getModelNames(), PairedSiteLikelihoods(), and setName().

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

Bpp/Phyl/Legacy/Likelihood/PairedSiteLikelihoods.h
Bpp/Phyl/Legacy/Likelihood/PairedSiteLikelihoods.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PairedSiteLikelihoods() [1/2]

◆ PairedSiteLikelihoods() [2/2]

◆ ~PairedSiteLikelihoods()

Member Function Documentation

◆ appendModel() [1/2]

◆ appendModel() [2/2]

◆ appendModels()

◆ bootstrap()

◆ computeExpectedLikelihoodWeights()

◆ getLikelihoods()

◆ getModelNames()

◆ getNumberOfModels()

◆ getNumberOfSites()

◆ setName()

Member Data Documentation

◆ logLikelihoods_

◆ modelNames_