bpp-phyl3  3.0.0
Public Types | Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
bpp::TransitionMatrixFromModel Class Reference

#include <Bpp/Phyl/Likelihood/DataFlow/Model.h>

+ Inheritance diagram for bpp::TransitionMatrixFromModel:
+ Collaboration diagram for bpp::TransitionMatrixFromModel:

Public Types

using Self = TransitionMatrixFromModel
 
using Dep = ConfiguredModel
 
using T = Eigen::MatrixXd
 

Public Member Functions

 TransitionMatrixFromModel (NodeRefVec &&deps, const Dimension< T > &dim)
 Build a new TransitionMatrixFromModel node with the given output dimensions. More...
 
std::string debugInfo () const final
 Node debug info (default = ""): user defined detailed info for DF graph debug. More...
 
bool compareAdditionalArguments (const Node_DF &other) const
 Compare node-specific configuration to another. More...
 
NodeRef derive (Context &c, const Node_DF &node) final
 Returns a node computing d(this_node_expression)/d(node_expression). More...
 
NodeRef recreate (Context &c, NodeRefVec &&deps) final
 Recreate the node with different dependencies. More...
 
std::string color () const final
 
std::string description () const final
 Node pretty name (default = type name). More...
 
std::string shape () const
 
const Eigen::MatrixXd & targetValue ()
 Access value, recompute if needed. More...
 
const Eigen::MatrixXd & accessValueConst () const noexcept
 Raw value access (const). More...
 
ValueRef< Eigen::MatrixXd > deriveAsValue (Context &c, const Node_DF &node)
 
void modify (Callable &&modifier, bool makeValid)
 General case for modification of the T object. More...
 
bool isValid () const noexcept
 
std::size_t nbDependentNodes () const noexcept
 Number of dependent nodes (ie nodes that depend on this) More...
 
const std::vector< Node_DF * > & dependentNodes () const noexcept
 
std::size_t nbDependencies () const noexcept
 Number of dependencies (ie nodes we depend on) More...
 
const NodeRefVec & dependencies () const noexcept
 
const NodeRef & dependency (std::size_t i) const noexcept
 
virtual bool hasNumericalProperty (NumericalProperty prop) const
 Test if the node has the given numerical property. More...
 
virtual std::size_t hashAdditionalArguments () const
 Return the hash of node-specific configuration. More...
 
void computeRecursively ()
 Compute this node value, recomputing dependencies (transitively) as needed. More...
 

Protected Member Functions

Eigen::MatrixXd & accessValueMutable () noexcept
 
void invalidateRecursively () noexcept
 Invalidate (transitively) dependent nodes from this one. More...
 
void makeInvalid () noexcept
 
void makeValid () noexcept
 
void resetDependencies_ (NodeRefVec &&dependenciesArg)
 

Private Member Functions

void compute () final
 Computation implementation. More...
 
void registerNode (Node_DF *n)
 
void unregisterNode (const Node_DF *n)
 

Private Attributes

Dimension< T > targetDimension_
 
Eigen::MatrixXd value_
 
NodeRefVec dependencyNodes_ {}
 
std::vector< Node_DF * > dependentNodes_ {}
 
bool isValid_ {false}
 

Detailed Description

transitionMatrix = f(model, branchLen, nDeriv, nMod, mult). transitionMatrix: Matrix(fromState, toState). model: ConfiguredModel. branchLen: double. nDeriv: degree of derivate (default: 0) nMod: in case of mixture model, takes the number of submodel where the generator comes from (optional, or null).

Node construction should be done with the create static method.

Definition at line 141 of file Model.h.

Member Typedef Documentation

◆ Dep

using bpp::TransitionMatrixFromModel::Dep = ConfiguredModel

Definition at line 145 of file Model.h.

◆ Self

using bpp::TransitionMatrixFromModel::Self = TransitionMatrixFromModel

Definition at line 144 of file Model.h.

◆ T

using bpp::TransitionMatrixFromModel::T = Eigen::MatrixXd

Definition at line 146 of file Model.h.

Constructor & Destructor Documentation

◆ TransitionMatrixFromModel()

TransitionMatrixFromModel::TransitionMatrixFromModel ( NodeRefVec &&  deps,
const Dimension< T > &  dim 
)

Build a new TransitionMatrixFromModel node with the given output dimensions.

Definition at line 134 of file Model.cpp.

Member Function Documentation

◆ accessValueConst()

const Eigen::MatrixXd & bpp::Value< Eigen::MatrixXd >::accessValueConst ( ) const
inlinenoexceptinherited

Raw value access (const).

Value is not guaranteed to be valid (no recomputation).

Definition at line 385 of file DataFlow.h.

◆ accessValueMutable()

Eigen::MatrixXd & bpp::Value< Eigen::MatrixXd >::accessValueMutable ( )
inlineprotectednoexceptinherited

Raw value access (mutable). Should only be used by subclasses to implement compute().

Definition at line 416 of file DataFlow.h.

◆ color()

std::string bpp::TransitionMatrixFromModel::color ( ) const
inlinefinalvirtual

Reimplemented from bpp::Node_DF.

Definition at line 162 of file Model.h.

◆ compareAdditionalArguments()

bool TransitionMatrixFromModel::compareAdditionalArguments ( const Node_DF &  other) const
virtual

Compare node-specific configuration to another.

Required by Context for merging. It must compare everything in the node configuration except its type and dependencies. See DataFlowNumeric for examples. The default returns false, so nodes are considered different and not merged.

Reimplemented from bpp::Node_DF.

Definition at line 148 of file Model.cpp.

◆ compute()

void TransitionMatrixFromModel::compute ( )
finalprivatevirtual

Computation implementation.

This functions is defined by derived classes. It should compute the new node value from dependency node values. When called, dependency node are guaranteed to have valid values.

This function is private to prevent use for invalid dependencies. Higher level functions like computeRecursively call it while ensuring dependency validity.

Compute has access to dependencies as a NodeRefVec (base Node_DF classes only). The recommended usage is to check dependency types at Node construction. Then use static_cast to access derived classes efficiently from the NodeRefVec. See DataFlowNumeric.h for examples.

Implements bpp::Node_DF.

Definition at line 189 of file Model.cpp.

References bpp::Value< Eigen::MatrixXd >::accessValueMutable(), bpp::copyBppToEigen(), bpp::Node_DF::dependency(), bpp::BranchModelInterface::getName(), bpp::Node_DF::nbDependencies(), and bpp::TextTools::toString().

◆ computeRecursively()

void bpp::Node_DF::computeRecursively ( )
inherited

Compute this node value, recomputing dependencies (transitively) as needed.

Not thread safe !

Definition at line 183 of file DataFlow.cpp.

References bpp::Node_DF::isValid().

Referenced by bpp::Value< T >::targetValue().

◆ debugInfo()

std::string TransitionMatrixFromModel::debugInfo ( ) const
finalvirtual

Node debug info (default = ""): user defined detailed info for DF graph debug.

Reimplemented from bpp::Node_DF.

Definition at line 139 of file Model.cpp.

References bpp::Value< Eigen::MatrixXd >::accessValueConst(), bpp::numeric::debug(), bpp::Node_DF::dependency(), targetDimension_, bpp::to_string(), and bpp::TextTools::toString().

◆ dependencies()

const NodeRefVec& bpp::Node_DF::dependencies ( ) const
inlinenoexceptinherited

Definition at line 183 of file DataFlow.h.

References bpp::Node_DF::dependencyNodes_.

Referenced by bpp::CWiseAdd< R, ReductionOf< T > >::compute(), bpp::CombineDeltaShifted< T >::compute(), bpp::CWiseMul< R, ReductionOf< T > >::compute(), bpp::ConfiguredDistribution::ConfiguredDistribution(), bpp::ConfiguredFrequencySet::ConfiguredFrequencySet(), bpp::ConfiguredModel::ConfiguredModel(), bpp::ConfiguredSimplex::ConfiguredSimplex(), bpp::ConfiguredTransitionMatrix::ConfiguredTransitionMatrix(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::derive(), and bpp::CWiseMul< R, ReductionOf< T > >::derive().

◆ dependency()

const NodeRef& bpp::Node_DF::dependency ( std::size_t  i) const
inlinenoexceptinherited

Definition at line 185 of file DataFlow.h.

References bpp::Node_DF::dependencyNodes_.

Referenced by bpp::BackwardHmmLikelihood_DF::BackwardHmmLikelihood_DF(), bpp::ForwardHmmLikelihood_DF::build(), bpp::ValueFromConfiguredParameter::color(), bpp::CWiseFill< R, T >::compute(), bpp::CWiseApply< R, T, F >::compute(), bpp::CWiseAdd< R, std::tuple< T0, T1 > >::compute(), bpp::CWiseAdd< R, T >::compute(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::compute(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::compute(), bpp::SumOfLogarithms< F >::compute(), bpp::CombineDeltaShifted< T >::compute(), bpp::CWiseSub< R, std::tuple< T0, T1 > >::compute(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::compute(), bpp::CWiseMean< R, ReductionOf< T >, P >::compute(), bpp::CWiseNegate< T >::compute(), bpp::CWiseInverse< T >::compute(), bpp::CWiseLog< T >::compute(), bpp::CWiseExp< T >::compute(), bpp::CWiseConstantPow< T >::compute(), bpp::ScalarProduct< R, T0, T1 >::compute(), bpp::LogSumExp< R, T0, T1 >::compute(), bpp::MatrixProduct< R, T0, T1 >::compute(), bpp::ShiftDelta< T >::compute(), bpp::Convert< R, F >::compute(), bpp::Identity< R >::compute(), bpp::ProbabilitiesFromDiscreteDistribution::compute(), bpp::ProbabilityFromDiscreteDistribution::compute(), bpp::CategoryFromDiscreteDistribution::compute(), bpp::FrequenciesFromFrequencySet::compute(), bpp::EquilibriumFrequenciesFromModel::compute(), compute(), bpp::TransitionFunctionFromModel::compute(), bpp::ProbabilitiesFromMixedModel::compute(), bpp::ProbabilityFromMixedModel::compute(), bpp::ShiftParameter::compute(), bpp::ValueFromConfiguredParameter::compute(), bpp::FrequenciesFromSimplex::compute(), bpp::EquilibriumFrequenciesFromTransitionMatrix::compute(), bpp::TransitionMatrixFromTransitionMatrix::compute(), bpp::CWisePattern< R >::compute(), bpp::CWiseMatching< R, ReductionOf< T > >::compute(), bpp::CWiseCompound< R, ReductionOf< T > >::compute(), bpp::ConfiguredParameter::compute(), bpp::CombineDeltaShifted< T >::create(), debugInfo(), bpp::TransitionFunctionFromModel::debugInfo(), bpp::ValueFromConfiguredParameter::debugInfo(), bpp::CondLikelihood::debugInfo(), bpp::CWiseFill< R, T >::derive(), bpp::CWisePattern< R >::derive(), bpp::CWiseMatching< R, ReductionOf< T > >::derive(), bpp::CWiseCompound< R, ReductionOf< T > >::derive(), bpp::CWiseApply< R, T, F >::derive(), bpp::CWiseAdd< R, std::tuple< T0, T1 > >::derive(), bpp::CWiseSub< R, std::tuple< T0, T1 > >::derive(), bpp::CWiseAdd< R, ReductionOf< T > >::derive(), bpp::CWiseAdd< R, T >::derive(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::derive(), bpp::CWiseMean< R, ReductionOf< T >, P >::derive(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::derive(), bpp::CWiseMul< R, ReductionOf< T > >::derive(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::derive(), bpp::CWiseNegate< T >::derive(), bpp::CWiseInverse< T >::derive(), bpp::CWiseLog< T >::derive(), bpp::CWiseExp< T >::derive(), bpp::CWiseConstantPow< T >::derive(), bpp::ScalarProduct< R, T0, T1 >::derive(), bpp::SumOfLogarithms< F >::derive(), bpp::LogSumExp< R, T0, T1 >::derive(), bpp::MatrixProduct< R, T0, T1 >::derive(), bpp::ShiftDelta< T >::derive(), bpp::CombineDeltaShifted< T >::derive(), bpp::Convert< R, F >::derive(), bpp::Identity< R >::derive(), bpp::ProbabilitiesFromDiscreteDistribution::derive(), bpp::ProbabilityFromDiscreteDistribution::derive(), bpp::CategoryFromDiscreteDistribution::derive(), bpp::FrequenciesFromFrequencySet::derive(), bpp::EquilibriumFrequenciesFromModel::derive(), derive(), bpp::TransitionFunctionFromModel::derive(), bpp::ProbabilitiesFromMixedModel::derive(), bpp::ProbabilityFromMixedModel::derive(), bpp::ShiftParameter::derive(), bpp::ValueFromConfiguredParameter::derive(), bpp::FrequenciesFromSimplex::derive(), bpp::EquilibriumFrequenciesFromTransitionMatrix::derive(), bpp::TransitionMatrixFromTransitionMatrix::derive(), bpp::BackwardHmmLikelihood_DF::derive(), bpp::ConfiguredParameter::derive(), bpp::ValueFromConfiguredParameter::description(), bpp::ConfiguredParameter::getValue(), bpp::ConfiguredParameter::recreate(), bpp::ConfiguredParameter::setValue(), and bpp::writeDotEdge().

◆ dependentNodes()

const std::vector<Node_DF*>& bpp::Node_DF::dependentNodes ( ) const
inlinenoexceptinherited

Definition at line 175 of file DataFlow.h.

References bpp::Node_DF::dependentNodes_.

◆ derive()

NodeRef TransitionMatrixFromModel::derive ( Context &  c,
const Node_DF &  node 
)
finalvirtual

Returns a node computing d(this_node_expression)/d(node_expression).

The expression represented by 'node' is considered as a variable. Event if 'node' is a constant value node, d(node)/d(node) == 1. The derivative of a matrix is the matrix of the derivatives. Derivation is undefined by default, and this function will throw an exception. Implementations will usually recursively derive sub-expressions and combine them.

Reimplemented from bpp::Node_DF.

Definition at line 153 of file Model.cpp.

References bpp::ConstantZero, bpp::NumericConstant< T >::create(), bpp::Node_DF::dependency(), bpp::Node_DF::nbDependencies(), and targetDimension_.

◆ deriveAsValue()

ValueRef<Eigen::MatrixXd > bpp::Value< Eigen::MatrixXd >::deriveAsValue ( Context &  c,
const Node_DF &  node 
)
inlineinherited

Derive and cast result as Value<T> (most nodes derive to the same value type).

Definition at line 389 of file DataFlow.h.

◆ description()

std::string bpp::TransitionMatrixFromModel::description ( ) const
inlinefinalvirtual

Node pretty name (default = type name).

Reimplemented from bpp::Node_DF.

Definition at line 167 of file Model.h.

◆ hashAdditionalArguments()

std::size_t bpp::Node_DF::hashAdditionalArguments ( ) const
virtualinherited

Return the hash of node-specific configuration.

Compute a hash from additional arguments of the node. The hashed values must the same as the ones compared by compareAdditionalArguments. The default returns 0, which is ok if there are no additional arguments.

Reimplemented in bpp::Sequence_DF, bpp::ConfiguredParameter, bpp::ConfiguredModel, bpp::NumericConstant< T >, bpp::ShiftParameter, bpp::ConstantOne< T >, bpp::ConstantZero< T >, bpp::CombineDeltaShifted< T >, bpp::ShiftDelta< T >, bpp::CWiseConstantPow< T >, bpp::ConfiguredTransitionMatrix, bpp::ConfiguredSimplex, bpp::ConfiguredFrequencySet, and bpp::ConfiguredDistribution.

Definition at line 171 of file DataFlow.cpp.

◆ hasNumericalProperty()

bool bpp::Node_DF::hasNumericalProperty ( NumericalProperty  prop) const
virtualinherited

Test if the node has the given numerical property.

This is an optional indication only, used for optimisations. If unsure, leave it to always false (the default implementation). This should be non recursive, to ensure a constant time check.

Reimplemented in bpp::NumericConstant< T >, bpp::ConstantOne< T >, and bpp::ConstantZero< T >.

Definition at line 168 of file DataFlow.cpp.

Referenced by bpp::ScalarProduct< R, T0, T1 >::create(), bpp::CWisePattern< R >::create(), bpp::CWiseAdd< R, T >::create(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::create(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::create(), bpp::CWiseNegate< T >::create(), bpp::CWiseInverse< T >::create(), bpp::CWiseLog< T >::create(), bpp::CWiseExp< T >::create(), bpp::CWiseConstantPow< T >::create(), and bpp::CombineDeltaShifted< T >::create().

◆ invalidateRecursively()

void bpp::Node_DF::invalidateRecursively ( )
protectednoexceptinherited

Invalidate (transitively) dependent nodes from this one.

Not thread safe !

Definition at line 219 of file DataFlow.cpp.

References bpp::Node_DF::isValid().

Referenced by bpp::Value< T >::modify(), and bpp::Node_DF::resetDependencies_().

◆ isValid()

bool bpp::Node_DF::isValid ( ) const
inlinenoexceptinherited

Definition at line 166 of file DataFlow.h.

References bpp::Node_DF::isValid_.

Referenced by bpp::Node_DF::computeRecursively(), bpp::Node_DF::invalidateRecursively(), and bpp::writeDotNode().

◆ makeInvalid()

void bpp::Node_DF::makeInvalid ( )
inlineprotectednoexceptinherited

Definition at line 270 of file DataFlow.h.

References bpp::Node_DF::isValid_.

Referenced by bpp::Node_DF::resetDependencies_().

◆ makeValid()

void bpp::Node_DF::makeValid ( )
inlineprotectednoexceptinherited

Definition at line 271 of file DataFlow.h.

References bpp::Node_DF::isValid_.

Referenced by bpp::Value< T >::modify(), bpp::NumericConstant< T >::NumericConstant(), bpp::NumericMutable< T >::NumericMutable(), and bpp::Sequence_DF::Sequence_DF().

◆ modify()

void bpp::Value< Eigen::MatrixXd >::modify ( Callable &&  modifier,
bool  makeValid 
)
inlineinherited

General case for modification of the T object.

Takes a callable object (lambda, function pointer) that performs the modification. It must take a single T& as argument, which will refer to the T object to modify. The callable is called exactly once.

Parameters
modifiercallable to modify this object
makeValidboolean if this object is valid after modification (which means no call to this->compute()

Definition at line 405 of file DataFlow.h.

◆ nbDependencies()

std::size_t bpp::Node_DF::nbDependencies ( ) const
inlinenoexceptinherited

Number of dependencies (ie nodes we depend on)

Definition at line 181 of file DataFlow.h.

References bpp::Node_DF::dependencyNodes_.

Referenced by bpp::SumOfLogarithms< F >::compute(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::compute(), bpp::CWiseMean< R, ReductionOf< T >, P >::compute(), bpp::EquilibriumFrequenciesFromModel::compute(), compute(), bpp::CWiseMatching< R, ReductionOf< T > >::compute(), bpp::CWiseCompound< R, ReductionOf< T > >::compute(), bpp::CWiseMatching< R, ReductionOf< T > >::derive(), bpp::CWiseCompound< R, ReductionOf< T > >::derive(), bpp::CWiseAdd< R, ReductionOf< T > >::derive(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::derive(), bpp::CWiseMean< R, ReductionOf< T >, P >::derive(), bpp::CWiseMul< R, ReductionOf< T > >::derive(), bpp::SumOfLogarithms< F >::derive(), bpp::CombineDeltaShifted< T >::derive(), bpp::EquilibriumFrequenciesFromModel::derive(), and derive().

◆ nbDependentNodes()

std::size_t bpp::Node_DF::nbDependentNodes ( ) const
inlinenoexceptinherited

Number of dependent nodes (ie nodes that depend on this)

Definition at line 172 of file DataFlow.h.

References bpp::Node_DF::dependentNodes_.

◆ recreate()

NodeRef TransitionMatrixFromModel::recreate ( Context &  c,
NodeRefVec &&  deps 
)
finalvirtual

Recreate the node with different dependencies.

Reimplemented from bpp::Node_DF.

Definition at line 184 of file Model.cpp.

References targetDimension_.

◆ registerNode()

void bpp::Node_DF::registerNode ( Node_DF *  n)
privateinherited

Definition at line 240 of file DataFlow.cpp.

References bpp::Node_DF::dependentNodes_.

◆ resetDependencies_()

void bpp::Node_DF::resetDependencies_ ( NodeRefVec &&  dependenciesArg)
inlineprotectedinherited

Definition at line 288 of file DataFlow.h.

References bpp::Node_DF::dependencyNodes_, bpp::Node_DF::invalidateRecursively(), and bpp::Node_DF::makeInvalid().

◆ shape()

std::string bpp::TransitionMatrixFromModel::shape ( ) const
inlinevirtual

Reimplemented from bpp::Node_DF.

Definition at line 172 of file Model.h.

◆ targetValue()

const Eigen::MatrixXd & bpp::Value< Eigen::MatrixXd >::targetValue ( )
inlineinherited

Access value, recompute if needed.

Recompute the value if it is not up to date. Then access it as const. Recomputation is single threaded and not thread safe.

Definition at line 374 of file DataFlow.h.

◆ unregisterNode()

void bpp::Node_DF::unregisterNode ( const Node_DF *  n)
privateinherited

Definition at line 245 of file DataFlow.cpp.

References bpp::Node_DF::dependentNodes_.

Member Data Documentation

◆ dependencyNodes_

NodeRefVec bpp::Node_DF::dependencyNodes_ {}
privateinherited

Definition at line 312 of file DataFlow.h.

Referenced by bpp::Node_DF::dependencies(), bpp::Node_DF::dependency(), bpp::Node_DF::nbDependencies(), bpp::Node_DF::Node_DF(), bpp::Node_DF::resetDependencies_(), and bpp::Node_DF::~Node_DF().

◆ dependentNodes_

std::vector<Node_DF*> bpp::Node_DF::dependentNodes_ {}
privateinherited

Definition at line 313 of file DataFlow.h.

Referenced by bpp::Node_DF::dependentNodes(), bpp::Node_DF::nbDependentNodes(), bpp::Node_DF::registerNode(), and bpp::Node_DF::unregisterNode().

◆ isValid_

bool bpp::Node_DF::isValid_ {false}
privateinherited

Definition at line 314 of file DataFlow.h.

Referenced by bpp::Node_DF::isValid(), bpp::Node_DF::makeInvalid(), and bpp::Node_DF::makeValid().

◆ targetDimension_

Dimension<T> bpp::TransitionMatrixFromModel::targetDimension_
private

Definition at line 149 of file Model.h.

Referenced by debugInfo(), derive(), and recreate().

◆ value_

Eigen::MatrixXd bpp::Value< Eigen::MatrixXd >::value_
privateinherited

Definition at line 419 of file DataFlow.h.

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