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/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 >()) throw (Exception)
	Build a new object from a site likelihoods array. More...

	~PairedSiteLikelihoods ()

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

void	appendModel (const bpp::TreeLikelihood &treelikelihood) throw (Exception)
	Append a model. More...

void	appendModels (const PairedSiteLikelihoods &psl) throw (Exception)
	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 throw (Exception)

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 60 of file PairedSiteLikelihoods.h.

Constructor & Destructor Documentation

◆ PairedSiteLikelihoods() [1/2]

PairedSiteLikelihoods::PairedSiteLikelihoods ( )

Definition at line 56 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>()`
	)
throw	(	Exception
	)

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 61 of file PairedSiteLikelihoods.cpp.

◆ ~PairedSiteLikelihoods()

bpp::PairedSiteLikelihoods::~PairedSiteLikelihoods ( )

inline

Definition at line 83 of file PairedSiteLikelihoods.h.

Member Function Documentation

◆ appendModel() [1/2]

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

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 87 of file PairedSiteLikelihoods.cpp.

Referenced by appendModel().

◆ appendModel() [2/2]

void PairedSiteLikelihoods::appendModel	(	const bpp::TreeLikelihood &	treelikelihood	)
throw	(	Exception
	)

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 99 of file PairedSiteLikelihoods.cpp.

References appendModel().

◆ appendModels()

void PairedSiteLikelihoods::appendModels	(	const PairedSiteLikelihoods &	psl	)
throw	(	Exception
	)

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 107 of file PairedSiteLikelihoods.cpp.

◆ 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 178 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 $W_m$ of a model is :

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