5 #ifndef BPP_PHYL_LIKELIHOOD_DATAFLOW_TRANSITIONMATRIX_H
6 #define BPP_PHYL_LIKELIHOOD_DATAFLOW_TRANSITIONMATRIX_H
13 #include <unordered_map>
41 throw bpp::Exception(
"ConfiguredTransitionMatrix clone should not happen.");
47 std::
string color () const final
72 std::unique_ptr<HmmTransitionMatrix>
hmm_;
87 using T = Eigen::VectorXd;
98 std::
string color () const final
120 using T = Eigen::MatrixXd;
143 return "TransitionMatrix";
const Parameter & parameter(const std::string &name) const override
const ParameterList & getParameters() const override
Context for dataflow node construction.
std::string debugInfo() const final
Node debug info (default = ""): user defined detailed info for DF graph debug.
Dimension< T > targetDimension_
void compute() final
Computation implementation.
bool compareAdditionalArguments(const Node_DF &other) const
Compare node-specific configuration to another.
EquilibriumFrequenciesFromTransitionMatrix(NodeRefVec &&deps, const Dimension< T > &dim)
NodeRef derive(Context &c, const Node_DF &node) final
Returns a node computing d(this_node_expression)/d(node_expression).
std::string color() const final
NodeRef recreate(Context &c, NodeRefVec &&deps) final
Recreate the node with different dependencies.
Base dataflow Node class.
Dimension< T > targetDimension_
std::string shape() const
std::string description() const final
Node pretty name (default = type name).
Abstract Node storing a value of type T.
Defines the basic types of data flow nodes.
std::vector< NodeRef > NodeRefVec
Alias for a dependency vector (of NodeRef).
std::shared_ptr< Node_DF > NodeRef
Store a dimension for type T.
Configuration for a numerical derivation: what delta to use, and type of derivation.