roadrunner  2.6.0
Fast simulator for SBML models
Public Member Functions | List of all members
rr::TimeSeriesSensitivitySolver Class Referenceabstract

generic interface for sensitivity solvers that integrate the model and compute sensitivities at each time point More...

#include <SensitivitySolver.h>

Inheritance diagram for rr::TimeSeriesSensitivitySolver:
rr::SensitivitySolver rr::Solver rr::Registrable rr::ForwardSensitivitySolver

Public Member Functions

virtual double integrate (double t0, double hstep)=0
 integrate the model from t0 to t0 + hstep. More...
 
virtual Matrix3D< double, double > solveSensitivities (double start, double stop, int num, std::vector< std::string > params, std::vector< std::string > species, int k)=0
 simulate a timeseries with sensitivities from start to step with num data points. More...
 
- Public Member Functions inherited from rr::SensitivitySolver
virtual rr::Matrix< double > getSensitivityMatrix (int k=0)=0
 get current values of sensitivities of model variables to parameters. More...
 
 Solver ()=default
 
 Solver (ExecutableModel *model)
 
- Public Member Functions inherited from rr::Solver
 Solver (ExecutableModel *model)
 
void updateSettings (Dictionary *inputSettings)
 Update settings values. More...
 
std::vector< std::string > getSettings () const
 Get a list of all settings for this solver. More...
 
std::unordered_map< std::string, Setting > & getSettingsMap ()
 get settings for this solver More...
 
virtual void resetSettings ()
 Reset all settings to their respective default values.
 
virtual Setting getValue (const std::string &key) const
 Get the value of an integrator setting. More...
 
virtual Setting hasValue (const std::string &key) const
 Return true if this setting is supported by the integrator. More...
 
virtual size_t getNumParams () const
 Get the number of parameters. More...
 
virtual std::string getParamName (size_t n) const
 Get the name of the parameter at index n. More...
 
virtual std::string getParamDisplayName (int n) const
 Get the display name of the parameter at index n. More...
 
virtual std::string getParamHint (int n) const
 Get the hint of the parameter at index n. More...
 
virtual std::string getParamDesc (int n) const
 Get the description of the parameter at index n. More...
 
virtual std::string getValueAsString (const std::string &key)
 Wrapper for getValue which converts output to a specific type. More...
 
virtual void setValue (const std::string &key, Setting value)
 
virtual std::string getSettingsRepr () const
 Get the solver settings as a std::string. More...
 
virtual std::string settingsPyDictRepr () const
 Python dictionary-style std::string representation of settings. More...
 
virtual std::string toString () const
 Return a std::string representation of the solver. More...
 
virtual std::string toRepr () const
 Return std::string representation a la Python repr method. More...
 
const std::string & getDisplayName (const std::string &key) const
 Gets the hint associated with a given key. More...
 
const std::string & getHint (const std::string &key) const
 Gets the hint associated with a given key. More...
 
const std::string & getDescription (const std::string &key) const
 Gets the description associated with a given key. More...
 
Setting::TypeId getType (const std::string &key) const
 Gets the type associated with a given key. More...
 
virtual void syncWithModel (ExecutableModel *m)=0
 Called whenever a new model is loaded to allow integrator to reset internal state. More...
 
virtual ExecutableModelgetModel () const
 returns the pointer to the ExecutableModel
 
virtual std::string getName () const=0
 Gets the name associated with this Solver type. More...
 
virtual std::string getHint () const=0
 Gets the hint associated with this Solver type. More...
 
virtual std::string getDescription () const=0
 Gets the description associated with this Solver type. More...
 
- Public Member Functions inherited from rr::Registrable
virtual std::string getName () const =0
 Gets the name associated with this Solver type. More...
 
virtual std::string getDescription () const =0
 Gets the description associated with this Solver type. More...
 
virtual std::string getHint () const =0
 Gets the hint associated with this Solver type. More...
 
virtual Solverconstruct (ExecutableModel *model) const =0
 Constructs a new Solver of a given type. More...
 

Additional Inherited Members

- Public Types inherited from rr::Solver
using SettingsList = std::vector< std::string >
 
using SettingsMap = std::unordered_map< std::string, Setting >
 
using DisplayNameMap = std::unordered_map< std::string, std::string >
 
using HintMap = std::unordered_map< std::string, std::string >
 
using DescriptionMap = std::unordered_map< std::string, std::string >
 
- Public Attributes inherited from rr::Solver
SettingsList sorted_settings
 
SettingsMap settings
 
DisplayNameMap display_names_
 
HintMap hints
 
DescriptionMap descriptions
 
- Protected Member Functions inherited from rr::Solver
void addSetting (const std::string &name, const Setting &val, const std::string &display_name, const std::string &hint, const std::string &description)
 
- Protected Attributes inherited from rr::Solver
ExecutableModelmModel = nullptr
 non-owning pointer to model
 

Detailed Description

generic interface for sensitivity solvers that integrate the model and compute sensitivities at each time point

Member Function Documentation

◆ integrate()

virtual double rr::TimeSeriesSensitivitySolver::integrate ( double  t0,
double  hstep 
)
pure virtual

integrate the model from t0 to t0 + hstep.

Note
this signature is the same as that found in Integrator().

integrating the model should update the sensitivities, which are available from getSensitivities()

Implemented in rr::ForwardSensitivitySolver.

◆ solveSensitivities()

virtual Matrix3D<double, double> rr::TimeSeriesSensitivitySolver::solveSensitivities ( double  start,
double  stop,
int  num,
std::vector< std::string >  params,
std::vector< std::string >  species,
int  k 
)
pure virtual

simulate a timeseries with sensitivities from start to step with num data points.

Matrix3D indexed by time. Each element of the 3D matrix is a Matrix<double> with rows and columns parameters and model variables respectively. The parameter k determines the kth order derivative of the sensitivity information that will be returned

Parameters
startstarting time for time series simulation
stoplast time point for time series simulation
numnumber of data points to simulate. Determines Z of Matrix3D.
paramsvector of parameters that you want sensitivity for. When empty (default), compute sensitivities for all parameters vs all variables.
speciesvector of species to include in the results. Note that unlike for params, reducing the number of species does not solve faster because the matrix slicing only occurs at the end. When empty (default) all species are returned.
k(default 0) return the kth other derivative of the sensitivity data.

Implemented in rr::ForwardSensitivitySolver.


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