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

Collaboration diagram for bpp::StochasticMapping:

Public Member Functions
	StochasticMapping (std::shared_ptr< LikelihoodCalculationSingleProcess > drl, size_t numOfMappings=10000)

	~StochasticMapping ()

	StochasticMapping (const StochasticMapping &sm)

StochasticMapping *	clone () const
	cloning function used by the copy constructor of ./Likelihood/JointLikelihoodFunction/h More...

void	generateStochasticMapping (std::vector< std::shared_ptr< PhyloTree >> &mappings)

std::shared_ptr< PhyloTree >	generateExpectedMapping (std::vector< std::shared_ptr< PhyloTree >> &mappings, size_t divMethod=0)
	Creates a single expected (i.e, average) history based on a given set of mappings steps. Correspond to Nielsen, Rasmus. "Mapping mutations on phylogenies." Systematic biology 51.5 (2002): 729-739.Ã¢ÂÂ More...

std::shared_ptr< PhyloTree >	generateAnalyticExpectedMapping (size_t divMethod=0)
	Creates a single expected (i.e, average) history based the rewards provided by the algorithm of Minin and Suchard (2008) the function assumes that there is only one site to simulate history for. More...

int	getNodeState (const PhyloNode *node) const

Protected Attributes
std::shared_ptr< LikelihoodCalculationSingleProcess >	likelihood_

std::shared_ptr< PhyloTree >	tree_

VVDouble	fractionalProbabilities_

VVVDouble	ConditionalProbabilities_

size_t	nodesCounter_

size_t	numOfMappings_

Private Member Functions
void	giveNamesToInternalNodes (PhyloTree &tree)

void	setNodeState (PhyloNode *node, size_t state)

void	setLeafsStates (std::shared_ptr< PhyloTree > mapping)

void	computeFractionals ()

void	ComputeConditionals ()

void	computeStatesFrequencies (VVDouble &ancestralStatesFreuquencies, vector< shared_ptr< PhyloTree >> &mappings)

size_t	sampleState (const VDouble &distibution)

void	sampleAncestrals (shared_ptr< PhyloTree > mapping)

void	setExpectedAncestrals (shared_ptr< PhyloTree > expectedMapping, VVDouble &posteriorProbabilities)

void	sampleMutationsGivenAncestrals (shared_ptr< PhyloTree > mapping)

void	updateBranchMapping (PhyloNode *son, const MutationPath &branchMapping)

void	sampleMutationsGivenAncestralsPerBranch (PhyloNode *son, size_t maxIterNum=10000)

void	updateBranchByDwellingTimes (PhyloNode *node, VDouble &dwellingTimes, VVDouble &posteriorProbabilities, size_t divMethod=0)

Detailed Description

Definition at line 39 of file StochasticMapping.h.

Constructor & Destructor Documentation

◆ StochasticMapping() [1/2]

StochasticMapping::StochasticMapping	(	std::shared_ptr< LikelihoodCalculationSingleProcess >	drl,
		size_t	numOfMappings = `10000`
	)

explicit

Definition at line 32 of file StochasticMapping.cpp.

References ComputeConditionals(), giveNamesToInternalNodes(), and tree_.

◆ ~StochasticMapping()

StochasticMapping::~StochasticMapping ( )

Definition at line 48 of file StochasticMapping.cpp.

◆ StochasticMapping() [2/2]

bpp::StochasticMapping::StochasticMapping ( const StochasticMapping & sm )

inline

Definition at line 81 of file StochasticMapping.h.

Member Function Documentation

◆ clone()

StochasticMapping* bpp::StochasticMapping::clone ( ) const

inline

cloning function used by the copy constructor of ./Likelihood/JointLikelihoodFunction/h

Definition at line 95 of file StochasticMapping.h.

◆ ComputeConditionals()

void StochasticMapping::ComputeConditionals ( )

private

Definition at line 384 of file StochasticMapping.cpp.

Referenced by StochasticMapping().

◆ computeFractionals()

void StochasticMapping::computeFractionals ( )

private

Definition at line 332 of file StochasticMapping.cpp.

◆ computeStatesFrequencies()

void StochasticMapping::computeStatesFrequencies	(	VVDouble &	ancestralStatesFreuquencies,
		vector< shared_ptr< PhyloTree >> &	mappings
	)

private

Definition at line 451 of file StochasticMapping.cpp.

◆ generateAnalyticExpectedMapping()

shared_ptr< PhyloTree > StochasticMapping::generateAnalyticExpectedMapping ( size_t divMethod = 0 )

Creates a single expected (i.e, average) history based the rewards provided by the algorithm of Minin and Suchard (2008) the function assumes that there is only one site to simulate history for.

Parameters

divMethod The method used in the case that the son and father share the same state (either divide the wdelling time of the staed state by 2 for two transitions (method 0) or allocate the entire dwelling time to be adjacent to the son(method 1))

Definition at line 157 of file StochasticMapping.cpp.

References tree_.

◆ generateExpectedMapping()

shared_ptr< PhyloTree > StochasticMapping::generateExpectedMapping	(	std::vector< std::shared_ptr< PhyloTree >> &	mappings,
		size_t	divMethod = `0`
	)

Creates a single expected (i.e, average) history based on a given set of mappings steps. Correspond to Nielsen, Rasmus. "Mapping mutations on phylogenies." Systematic biology 51.5 (2002): 729-739.Ã¢ÂÂ

the function assumes that there is only one site to simulate history

Parameters

mappings	A vector of stochastic mappings to average
divMethod	The method used in the case that the son and father share the same state (either divide the dwelling time of the staed state by 2 for two transitions (method 0) or allocate the entire dwelling time to be adjacent to the son(method 1))

Definition at line 93 of file StochasticMapping.cpp.

References tree_.

◆ generateStochasticMapping()

void StochasticMapping::generateStochasticMapping ( std::vector< std::shared_ptr< PhyloTree >> & mappings )

Definition at line 53 of file StochasticMapping.cpp.

References numOfMappings_.

◆ getNodeState()

int StochasticMapping::getNodeState ( const PhyloNode * node ) const

Definition at line 286 of file StochasticMapping.cpp.

References bpp::PhyloNode::getProperty(), and STATE.

◆ giveNamesToInternalNodes()

void StochasticMapping::giveNamesToInternalNodes ( PhyloTree & tree )

private

Definition at line 301 of file StochasticMapping.cpp.

References bpp::AssociationTreeGraphImplObserver< class, class, class >::getAllInnerNodes(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNodeIndex(), and bpp::TextTools::toString().

Referenced by StochasticMapping().

◆ sampleAncestrals()

void StochasticMapping::sampleAncestrals ( shared_ptr< PhyloTree > mapping )

private

Definition at line 521 of file StochasticMapping.cpp.

◆ sampleMutationsGivenAncestrals()

void StochasticMapping::sampleMutationsGivenAncestrals ( shared_ptr< PhyloTree > mapping )

private

Definition at line 548 of file StochasticMapping.cpp.

◆ sampleMutationsGivenAncestralsPerBranch()

void StochasticMapping::sampleMutationsGivenAncestralsPerBranch	(	PhyloNode *	son,
		size_t	maxIterNum = `10000`
	)

private

Definition at line 600 of file StochasticMapping.cpp.

◆ sampleState()

size_t StochasticMapping::sampleState ( const VDouble & distibution )

private

Definition at line 502 of file StochasticMapping.cpp.

◆ setExpectedAncestrals()

void StochasticMapping::setExpectedAncestrals	(	shared_ptr< PhyloTree >	expectedMapping,
		VVDouble &	posteriorProbabilities
	)

private

Definition at line 76 of file StochasticMapping.cpp.

◆ setLeafsStates()

void StochasticMapping::setLeafsStates ( std::shared_ptr< PhyloTree > mapping )

private

Definition at line 313 of file StochasticMapping.cpp.

◆ setNodeState()

void StochasticMapping::setNodeState	(	PhyloNode *	node,
		size_t	state
	)

private

Definition at line 293 of file StochasticMapping.cpp.

References bpp::PhyloNode::setProperty(), and STATE.

◆ updateBranchByDwellingTimes()

void StochasticMapping::updateBranchByDwellingTimes	(	PhyloNode *	node,
		VDouble &	dwellingTimes,
		VVDouble &	posteriorProbabilities,
		size_t	divMethod = `0`
	)

private

Definition at line 656 of file StochasticMapping.cpp.

◆ updateBranchMapping()

void StochasticMapping::updateBranchMapping	(	PhyloNode *	son,
		const MutationPath &	branchMapping
	)

private

Definition at line 565 of file StochasticMapping.cpp.

Member Data Documentation

◆ ConditionalProbabilities_

VVVDouble bpp::StochasticMapping::ConditionalProbabilities_

protected

Definition at line 70 of file StochasticMapping.h.

◆ fractionalProbabilities_

VVDouble bpp::StochasticMapping::fractionalProbabilities_

protected

Definition at line 68 of file StochasticMapping.h.

◆ likelihood_

std::shared_ptr<LikelihoodCalculationSingleProcess> bpp::StochasticMapping::likelihood_

protected

Definition at line 49 of file StochasticMapping.h.

◆ nodesCounter_

size_t bpp::StochasticMapping::nodesCounter_

protected

Definition at line 71 of file StochasticMapping.h.

◆ numOfMappings_

size_t bpp::StochasticMapping::numOfMappings_

protected

Definition at line 72 of file StochasticMapping.h.

Referenced by generateStochasticMapping().

◆ tree_

std::shared_ptr<PhyloTree> bpp::StochasticMapping::tree_

protected

Definition at line 51 of file StochasticMapping.h.

Referenced by generateAnalyticExpectedMapping(), generateExpectedMapping(), and StochasticMapping().

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

Bpp/Phyl/Mapping/StochasticMapping.h
Bpp/Phyl/Mapping/StochasticMapping.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ StochasticMapping() [1/2]

◆ ~StochasticMapping()

◆ StochasticMapping() [2/2]

Member Function Documentation

◆ clone()

◆ ComputeConditionals()

◆ computeFractionals()

◆ computeStatesFrequencies()

◆ generateAnalyticExpectedMapping()

◆ generateExpectedMapping()

◆ generateStochasticMapping()

◆ getNodeState()

◆ giveNamesToInternalNodes()

◆ sampleAncestrals()

◆ sampleMutationsGivenAncestrals()

◆ sampleMutationsGivenAncestralsPerBranch()

◆ sampleState()

◆ setExpectedAncestrals()

◆ setLeafsStates()

◆ setNodeState()

◆ updateBranchByDwellingTimes()

◆ updateBranchMapping()

Member Data Documentation

◆ ConditionalProbabilities_

◆ fractionalProbabilities_

◆ likelihood_

◆ nodesCounter_

◆ numOfMappings_

◆ tree_