Organization of submodels in mixed substitution models as paths. More...

#include <Bpp/Phyl/Likelihood/ModelScenario.h>

Collaboration diagram for bpp::ModelScenario:

Public Member Functions
	ModelScenario ()

virtual	~ModelScenario ()

	ModelScenario (std::vector< std::shared_ptr< ModelPath >> vModelPaths)

	ModelScenario (const ModelScenario &set)

ModelScenario &	operator= (const ModelScenario &set)

void	clear ()
	Resets the list of the ModelPaths. More...

void	addModelPath (std::shared_ptr< ModelPath > hn)

void	changeModel (std::shared_ptr< MixedTransitionModelInterface > m1, std::shared_ptr< MixedTransitionModelInterface > m2)

bool	complete ()

size_t	getNumberOfModelPaths () const

std::shared_ptr< ModelPath >	getModelPath (size_t i)

std::shared_ptr< const ModelPath >	getModelPath (size_t i) const

std::vector< std::shared_ptr< MixedTransitionModelInterface > >	getModels () const
	return models found in several paths More...

bool	hasExclusivePaths () const
	Checks if all the path (ie hypernodes) are exclusive. More...

void	computeModelPathsProbabilities ()
	compute the probabilities in all the ModelPaths More...

std::string	toString () const
	string description More...

Private Attributes
std::vector< std::shared_ptr< ModelPath > >	vModelPaths_

Detailed Description

Organization of submodels in mixed substitution models as paths.

These sets are defined through an hypergraph, denoted as a scenario, ie a list of hypernodes. HyperNodes are defined in class ModelPath.

For example, suppose there are 3 mixed models (M1,M2 and M3), with 2, 3, 4 submodels (S1, S2, ...) each.

If the sites are allowed to follow any combination of submodels (12 combinations) the corresponding scenario has only one model path: (<1,2>,<1,2,3>,<1,2,3,4>).

The scenario with model paths ((<1>,<1,2>,<1,2>),(<2>,<3>,<3,4>)) means that a site either follows 6 combinations:

M1:S1 and ( M2:S1 or M2:S2 ) and ( M3:S1 or M3:S2 ).

or

M1:S2 and M2:S3 and (M3:S3 or M3:S4).

If a mixed model is not represented in any model path, it is considered as non-mixed, which means that his transition probabilities are the mixture of the transition probabilities of its submodels.

Dependency of the submodels entails constraints in the probabilities of the submodels, and definition of the model paths must be taken with care for the whole modelling to be possible.

In this implementation, for sake of simplification (and for reason of time), each submodel must belong to exactly one given model path, but in theory more complex dependencies are possible.

Inside each path model, for each set of submodels, the probabilities of the submodels are conditional probabilities, which means that they sum 1 and their ratio are unchanged.

For instance, for scenario ((<1>,<1,2>,<1,2>),(<2>,<3>,<3,4>)), the probabilities of model paths are the probabilities of M1:S1 and M1:S2. In the first model path, the probabilities of M2:S1 and M2:S2 are P(M2:S1)/(P(M2:S1)+P(M2:S2)) and P(M2:S2)/(P(M2:S1)+P(M2:S2)).

We do not certify that the probability parameters of the mixed models are all useful, and then identifiability problems may be encountered.

There is a method ("complete") that creates an additional model path to ensure that all submodels belong to at least an model path.

To do (perhaps) : compute the probabilities of the hypernodes from a specific mixed model

Definition at line 80 of file ModelScenario.h.

Constructor & Destructor Documentation

◆ ModelScenario() [1/3]

bpp::ModelScenario::ModelScenario ( )

inline

Definition at line 86 of file ModelScenario.h.

◆ ~ModelScenario()

virtual bpp::ModelScenario::~ModelScenario ( )

inlinevirtual

Definition at line 89 of file ModelScenario.h.

◆ ModelScenario() [2/3]

bpp::ModelScenario::ModelScenario ( std::vector< std::shared_ptr< ModelPath >> vModelPaths )

inline

Definition at line 91 of file ModelScenario.h.

◆ ModelScenario() [3/3]

bpp::ModelScenario::ModelScenario ( const ModelScenario & set )

inline

Definition at line 95 of file ModelScenario.h.

Member Function Documentation

◆ addModelPath()

void bpp::ModelScenario::addModelPath ( std::shared_ptr< ModelPath > hn )

inline

Definition at line 119 of file ModelScenario.h.

References vModelPaths_.

◆ changeModel()

void ModelScenario::changeModel	(	std::shared_ptr< MixedTransitionModelInterface >	m1,
		std::shared_ptr< MixedTransitionModelInterface >	m2
	)

Definition at line 40 of file ModelScenario.cpp.

◆ clear()

void bpp::ModelScenario::clear ( )

inline

Resets the list of the ModelPaths.

Definition at line 110 of file ModelScenario.h.

References vModelPaths_.

◆ complete()

bool ModelScenario::complete ( )

Definition at line 12 of file ModelScenario.cpp.

References bpp::ModelPath::getModels().

◆ computeModelPathsProbabilities()

void ModelScenario::computeModelPathsProbabilities ( )

compute the probabilities in all the ModelPaths

The probabilities of the hypernodes are computed from the lead mixed model of the FIRST ModelPath (and not of the others).

Definition at line 74 of file ModelScenario.cpp.

References bpp::ModelPath::getPathNode(), bpp::ModelPath::getProbability(), bpp::ModelPath::hasModel(), bpp::ModelPath::setProbability(), and bpp::TextTools::toString().

◆ getModelPath() [1/2]

std::shared_ptr<ModelPath> bpp::ModelScenario::getModelPath ( size_t i )

inline

Definition at line 159 of file ModelScenario.h.

References vModelPaths_.

Referenced by bpp::ProcessComputationTree::buildFollowingScenario_().

◆ getModelPath() [2/2]

std::shared_ptr<const ModelPath> bpp::ModelScenario::getModelPath ( size_t i ) const

inline

Definition at line 161 of file ModelScenario.h.

References vModelPaths_.

◆ getModels()

vector< shared_ptr< MixedTransitionModelInterface > > ModelScenario::getModels ( ) const

return models found in several paths

Definition at line 170 of file ModelScenario.cpp.

◆ getNumberOfModelPaths()

size_t bpp::ModelScenario::getNumberOfModelPaths ( ) const

inline

Definition at line 157 of file ModelScenario.h.

References vModelPaths_.

Referenced by bpp::ProcessComputationTree::buildFollowingScenario_().

◆ hasExclusivePaths()

bool ModelScenario::hasExclusivePaths ( ) const

Checks if all the path (ie hypernodes) are exclusive.

Definition at line 49 of file ModelScenario.cpp.

References bpp::ModelPath::intersects().

◆ operator=()

ModelScenario& bpp::ModelScenario::operator= ( const ModelScenario & set )

inline

Definition at line 99 of file ModelScenario.h.

References vModelPaths_.

◆ toString()

string ModelScenario::toString ( ) const

string description

Definition at line 158 of file ModelScenario.cpp.

Member Data Documentation

◆ vModelPaths_

std::vector< std::shared_ptr<ModelPath> > bpp::ModelScenario::vModelPaths_

private

Definition at line 83 of file ModelScenario.h.

Referenced by addModelPath(), clear(), getModelPath(), getNumberOfModelPaths(), and operator=().

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

Bpp/Phyl/Likelihood/ModelScenario.h
Bpp/Phyl/Likelihood/ModelScenario.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ModelScenario() [1/3]

◆ ~ModelScenario()

◆ ModelScenario() [2/3]

◆ ModelScenario() [3/3]

Member Function Documentation

◆ addModelPath()

◆ changeModel()

◆ clear()

◆ complete()

◆ computeModelPathsProbabilities()

◆ getModelPath() [1/2]

◆ getModelPath() [2/2]

◆ getModels()

◆ getNumberOfModelPaths()

◆ hasExclusivePaths()

◆ operator=()

◆ toString()

Member Data Documentation

◆ vModelPaths_