bpp::RewardMappingTools Class Reference

Provide methods to compute reward mappings. More...

#include <Bpp/Phyl/Mapping/RewardMappingTools.h>

Public Member Functions
	RewardMappingTools ()
virtual	~RewardMappingTools ()

Static Public Member Functions
static std::unique_ptr< ProbabilisticRewardMapping >	computeRewardVectors (LikelihoodCalculationSingleProcess &rltc, const std::vector< uint > &edgeIds, Reward &reward, short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, bool verbose=true)
	Compute the reward vectors for a particular dataset using the double-recursive likelihood computation. More...
static void	writeToStream (const ProbabilisticRewardMapping &rewards, const AlignmentDataInterface &sites, std::ostream &out)
	Write the reward vectors to a stream. More...
static void	readFromStream (std::istream &in, ProbabilisticRewardMapping &rewards)
	Read the reward vectors from a stream. More...
static double	computeSumForBranch (const ProbabilisticRewardMapping &smap, size_t branchIndex)
	Sum all rewards of a given branch (specified by its index). More...
static double	computeSumForSite (const ProbabilisticRewardMapping &smap, size_t siteIndex)
	Sum all rewards on a given site (specified by its index). More...

Detailed Description

Provide methods to compute reward mappings.

For now, 4 methods are implemented, and provide reward mappings.

See: Minin, V.N. and Suchard, M.A., Fast, accurate and simulation-free stochastic mapping Philosophical Transactions of the Royal Society B 2008 363:3985-95.

Author

Laurent Guéguen

Definition at line 28 of file RewardMappingTools.h.

Constructor & Destructor Documentation

RewardMappingTools()

bpp::RewardMappingTools::RewardMappingTools ( )

inline

Definition at line 31 of file RewardMappingTools.h.

~RewardMappingTools()

virtual bpp::RewardMappingTools::~RewardMappingTools ( )

inlinevirtual

Definition at line 32 of file RewardMappingTools.h.

Member Function Documentation

computeRewardVectors()

unique_ptr< ProbabilisticRewardMapping > RewardMappingTools::computeRewardVectors ( LikelihoodCalculationSingleProcess &  rltc, const std::vector< uint > &  edgeIds, Reward &  reward, short  unresolvedOption = SubstitutionMappingTools::UNRESOLVED_ZERO, bool  verbose = true  )

static

Compute the reward vectors for a particular dataset using the double-recursive likelihood computation.

Parameters

rltc	A LikelihoodCalculationSingleProcess object.
edgeIds	The Ids of the nodes the reward vectors are computed on.
reward	The Reward to use.
unresolvedOption	Describes how unresolved are managed (see above).
verbose	Print info to screen.

Returns

A vector of reward vectors (one for each site).

Exceptions

Exception

If the likelihood object is not initialized.

Definition at line 25 of file RewardMappingTools.cpp.

References bpp::Reward::clone(), bpp::VectorTools::contains(), bpp::numeric::convert(), bpp::numeric::cwise(), bpp::ApplicationTools::displayGauge(), bpp::ApplicationTools::displayTask(), bpp::ApplicationTools::displayTaskDone(), bpp::LikelihoodCalculationSingleProcess::getBackwardLikelihoodsAtEdgeForClass(), bpp::LikelihoodCalculationSingleProcess::getEdgesIds(), bpp::LikelihoodCalculationSingleProcess::getForwardLikelihoodsAtNodeForClass(), bpp::LikelihoodCalculationSingleProcess::getForwardLikelihoodTree(), bpp::LikelihoodCalculationSingleProcess::getLikelihoodsAtNodeForClass(), bpp::SubstitutionProcessInterface::getNumberOfClasses(), bpp::LikelihoodCalculationSingleProcess::getNumberOfDistinctSites(), bpp::SubstitutionProcessInterface::getParametrizablePhyloTree(), bpp::ProbabilityDAG::getProbaAtNode(), bpp::SubstitutionProcessInterface::getProbabilityForModel(), bpp::LikelihoodCalculationSingleProcess::getRootArrayPositions(), bpp::LikelihoodCalculationSingleProcess::getTreeNode(), bpp::LikelihoodCalculation::isInitialized(), bpp::ApplicationTools::message, bpp::SubstitutionProcessInterface::parametrizablePhyloTree(), bpp::LikelihoodCalculationSingleProcess::substitutionProcess(), bpp::TextTools::toString(), bpp::SubstitutionMappingTools::UNRESOLVED_AVERAGE, bpp::SubstitutionMappingTools::UNRESOLVED_ZERO, and bpp::ExtendedFloatEigen< R, C, EigenType >::Zero().

computeSumForBranch()

double RewardMappingTools::computeSumForBranch ( const ProbabilisticRewardMapping &  smap, size_t  branchIndex  )

static

Sum all rewards of a given branch (specified by its index).

Parameters

smap	The reward map to use.
branchIndex	The index of the reward vector for which the counts should be computed.

Returns

A vector will all rewards summed.

Definition at line 324 of file RewardMappingTools.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdge(), bpp::AbstractMapping::getNumberOfSites(), and bpp::ProbabilisticRewardMapping::getSiteIndex().

computeSumForSite()

double RewardMappingTools::computeSumForSite ( const ProbabilisticRewardMapping &  smap, size_t  siteIndex  )

static

Sum all rewards on a given site (specified by its index).

Parameters

smap	The substitution map to use.
siteIndex	The index of the substitution vector for which the counts should be computed.

Returns

A vector will all counts summed for each types of substitutions.

Definition at line 339 of file RewardMappingTools.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::allEdgesIterator(), and bpp::ProbabilisticRewardMapping::getSiteIndex().

readFromStream()

void RewardMappingTools::readFromStream ( std::istream &  in, ProbabilisticRewardMapping &  rewards  )

static

Read the reward vectors from a stream.

Parameters

in	The input stream where to read the vectors.
rewards	The mapping object to fill.

Exceptions

IOException

If an input error happens.

Definition at line 279 of file RewardMappingTools.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::allEdgesIterator(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeIndex(), bpp::DataTable::read(), bpp::ProbabilisticRewardMapping::setNumberOfSites(), bpp::AbstractMapping::setSitePosition(), bpp::TextTools::toDouble(), and bpp::Exception::what().

writeToStream()

void RewardMappingTools::writeToStream ( const ProbabilisticRewardMapping &  rewards, const AlignmentDataInterface &  sites, std::ostream &  out  )

static

Write the reward vectors to a stream.

Parameters

rewards	The reward vectors to write.
sites	The dataset associated to the vectors (needed to know the position of each site in the dataset).
out	The output stream where to write the vectors.

Exceptions

IOException

If an output error happens.

Definition at line 245 of file RewardMappingTools.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::allEdgesIterator(), bpp::CoreSiteInterface::getCoordinate(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeIndex(), bpp::AbstractMapping::getNumberOfSites(), bpp::ProbabilisticRewardMapping::getSiteIndex(), and bpp::TemplateAlignmentDataInterface< class >::site().

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

• Bpp/Phyl/Mapping/RewardMappingTools.h
• Bpp/Phyl/Mapping/RewardMappingTools.cpp