bpp::SubstitutionModelSetTools Class Reference

Tools for automatically creating SubstitutionModelSet objects. More...

#include <Bpp/Phyl/Legacy/Model/SubstitutionModelSetTools.h>

Static Public Member Functions
static std::unique_ptr< SubstitutionModelSet >	createHomogeneousModelSet (std::shared_ptr< TransitionModelInterface > model, std::shared_ptr< FrequencySetInterface > rootFreqs, const Tree &tree)
	Create a SubstitutionModelSet object, corresponding to the homogeneous case. More...
static std::unique_ptr< SubstitutionModelSet >	createNonHomogeneousModelSet (std::shared_ptr< TransitionModelInterface > model, std::shared_ptr< FrequencySetInterface > rootFreqs, const Tree &tree, const std::map< std::string, std::string > &aliasFreqNames, const std::map< std::string, std::vector< Vint >> &globalParameterNames)
	Create a SubstitutionModelSet object, with one model per branch. More...

Detailed Description

Tools for automatically creating SubstitutionModelSet objects.

Definition at line 21 of file SubstitutionModelSetTools.h.

Member Function Documentation

createHomogeneousModelSet()

unique_ptr< SubstitutionModelSet > SubstitutionModelSetTools::createHomogeneousModelSet ( std::shared_ptr< TransitionModelInterface >  model, std::shared_ptr< FrequencySetInterface >  rootFreqs, const Tree &  tree  )

static

Create a SubstitutionModelSet object, corresponding to the homogeneous case.

This class is mainly for testing purpose.

Parameters

model	The model to use.
rootFreqs	A FrequencySet object to parametrize root frequencies.
tree	The tree to use for the construction of the set.

Definition at line 13 of file SubstitutionModelSetTools.cpp.

References bpp::Tree::getNodesId(), and bpp::Tree::getRootId().

Referenced by bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator().

createNonHomogeneousModelSet()

unique_ptr< SubstitutionModelSet > SubstitutionModelSetTools::createNonHomogeneousModelSet ( std::shared_ptr< TransitionModelInterface >  model, std::shared_ptr< FrequencySetInterface >  rootFreqs, const Tree &  tree, const std::map< std::string, std::string > &  aliasFreqNames, const std::map< std::string, std::vector< Vint >> &  globalParameterNames  )

static

Create a SubstitutionModelSet object, with one model per branch.

All branches share the same type of model, but allow one set of parameters per branch. This is also possible to specify some parameters to be common to all branches.

Parameters

model	The model to use.
rootFreqs	A FrequencySet object to parametrize root frequencies.
tree	The tree to use for the construction of the set.
aliasFreqNames	Aliases for the frequencies names
globalParameterNames	map for shared parameters. Associated value is a vector of vectors of branch ids that share the parameter. If the vector is empty, the parameter is shared among all branches.

All other parameters will be considered distinct for all branches.

Definition at line 46 of file SubstitutionModelSetTools.cpp.

References bpp::Parameter::getName(), bpp::Tree::getNodesId(), bpp::ParameterList::getParameterNames(), bpp::Tree::getRootId(), bpp::ApplicationTools::matchingParameters(), bpp::ParameterList::size(), and bpp::TextTools::toString().

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

• Bpp/Phyl/Legacy/Model/SubstitutionModelSetTools.h
• Bpp/Phyl/Legacy/Model/SubstitutionModelSetTools.cpp