libRoadRunner C API  1.0.0
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Functions
Stochastic simulations

Stochastic simulation algorithms. More...

Functions

bool getSeed (RRHandle handle, long *seed)
 Determine the current seed used by the random generator. More...
 
bool setSeed (RRHandle handle, long seed)
 Set the current seed used by the random generator. More...
 
RRCDataPtr gillespie (RRHandle handle)
 Carry out a time-course simulation using the Gillespie algorithm with variable step size. setTimeStart, setTimeEnd, etc are used to set the simulation characteristics. More...
 
RRCDataPtr gillespieEx (RRHandle handle, double timeStart, double timeEnd)
 Carry out a time-course simulation using the Gillespie algorithm based on the given arguments, time start, time end and number of points. More...
 
RRCDataPtr gillespieOnGrid (RRHandle handle)
 Carry out a time-course simulation using the Gillespie algorithm with fixed step size. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics. More...
 
RRCDataPtr gillespieOnGridEx (RRHandle handle, double timeStart, double timeEnd, int numberOfPoints)
 Carry out a time-course simulation using the Gillespie algorithm with fixed step size based on the given arguments, time start, time end, and number of points. More...
 
RRCDataPtr gillespieMeanOnGrid (RRHandle handle, int numberOfSimulations)
 Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average of the simulations. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics. More...
 
RRCDataPtr gillespieMeanOnGridEx (RRHandle handle, double timeStart, double timeEnd, int numberOfPoints, int numberOfSimulations)
 Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average of the simulations. Based on the given arguments, time start, time end, and number of points. More...
 
RRCDataPtr gillespieMeanSDOnGrid (RRHandle handle, int numberOfSimulations)
 Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average and standard deviation of the simulations. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics. More...
 
RRCDataPtr gillespieMeanSDOnGridEx (RRHandle handle, double timeStart, double timeEnd, int numberOfSteps, int numberOfSimulations)
 Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average and standard deviation of the simulations. Based on the given arguments, time start, time end, number of points, and number of simulations. More...
 

Detailed Description

Stochastic simulation algorithms.

Function Documentation

bool getSeed ( RRHandle  handle,
long *  seed 
)

Determine the current seed used by the random generator.

Parameters
[in]handleHandle to a RoadRunner instance
[out]seedThis is the value of the current seed, returned to the caller
Returns
Returns true if successful
RRCDataPtr gillespie ( RRHandle  handle)

Carry out a time-course simulation using the Gillespie algorithm with variable step size. setTimeStart, setTimeEnd, etc are used to set the simulation characteristics.

Parameters
[in]handleHandle to a RoadRunner instance
Returns
Returns an array (RRCDataPtr) of columns containing the results of the simulation including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.
RRCDataPtr gillespieEx ( RRHandle  handle,
double  timeStart,
double  timeEnd 
)

Carry out a time-course simulation using the Gillespie algorithm based on the given arguments, time start, time end and number of points.

Example:

1 RRCDataPtr m;
2 
3 double timeStart = 0.0;
4 double timeEnd = 25;
5 
6 m = gillespieEx (rrHandle, timeStart, timeEnd);
Parameters
[in]handleHandle to a RoadRunner instance
[in]timeStartTime start
[in]timeEndTime end
Returns
Returns an array (RRCDataPtr) of columns containing the results of the simulation including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.
RRCDataPtr gillespieMeanOnGrid ( RRHandle  handle,
int  numberOfSimulations 
)

Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average of the simulations. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics.

Parameters
[in]handleHandle to a RoadRunner instance
[in]numberOfSimulationsNumber of simulations to perform
Returns
Returns an array (RRCDataPtr) of columns containing the average of the results of the simulations including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.
RRCDataPtr gillespieMeanOnGridEx ( RRHandle  handle,
double  timeStart,
double  timeEnd,
int  numberOfPoints,
int  numberOfSimulations 
)

Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average of the simulations. Based on the given arguments, time start, time end, and number of points.

Example:

1 RRCDataPtr m;
2 
3 double timeStart = 0.0;
4 double timeEnd = 25;
5 int numberOfPoints = 200;
6 int numberOfSimulations = 10;
7 
8 m = gillespieMeanOnGridEx (rrHandle, timeStart, timeEnd, numberOfPoints, numberOfSimulations);
Parameters
[in]handleHandle to a RoadRunner instance
[in]timeStartTime start
[in]timeEndTime end
[in]numberOfPointsFixed number of points to generate
[in]numberOfSimulationsNumber of simulations to perform
Returns
Returns an array (RRCDataPtr) of columns containing the average of the results of the simulation including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.
RRCDataPtr gillespieMeanSDOnGrid ( RRHandle  handle,
int  numberOfSimulations 
)

Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average and standard deviation of the simulations. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics.

Parameters
[in]handleHandle to a RoadRunner instance
[in]numberOfSimulationsNumber of simulations to perform
Returns
Returns an array (RRCDataPtr) of columns containing the average of the results of the simulations including string labels for the individual columns. The averages are in Data and the standard deviations are in Weights. The client is responsible for freeing the resulting RRCDataPtr structure.
RRCDataPtr gillespieMeanSDOnGridEx ( RRHandle  handle,
double  timeStart,
double  timeEnd,
int  numberOfSteps,
int  numberOfSimulations 
)

Carry out a series of time-course simulations using the Gillespie algorithm with fixed step size, then return the average and standard deviation of the simulations. Based on the given arguments, time start, time end, number of points, and number of simulations.

Example:

1 RRCDataPtr m;
2 
3 double timeStart = 0.0;
4 double timeEnd = 25;
5 int numberOfPoints = 200;
6 int numberOfSimulations = 10;
7 
8 m = gillespieMeanSDOnGridEx (rrHandle, timeStart, timeEnd, numberOfPoints, numberOfSimulations);
Parameters
[in]handleHandle to a RoadRunner instance
[in]timeStartTime start
[in]timeEndTime end
[in]numberOfPointsFixed number of points to generate
[in]numberOfSimulationsNumber of simulations to perform
Returns
Returns an array (RRCDataPtr) of columns containing the average of the results of the simulation including string labels for the individual columns. The average values are in Data and the standard deviations are in Weights. The client is responsible for freeing the resulting RRCDataPtr structure.
RRCDataPtr gillespieOnGrid ( RRHandle  handle)

Carry out a time-course simulation using the Gillespie algorithm with fixed step size. setTimeStart, setTimeEnd, setNumPoints, etc are used to set the simulation characteristics.

Parameters
[in]handleHandle to a RoadRunner instance
Returns
Returns an array (RRCDataPtr) of columns containing the results of the simulation including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.
RRCDataPtr gillespieOnGridEx ( RRHandle  handle,
double  timeStart,
double  timeEnd,
int  numberOfPoints 
)

Carry out a time-course simulation using the Gillespie algorithm with fixed step size based on the given arguments, time start, time end, and number of points.

Example:

1 RRCDataPtr m;
2 
3 double timeStart = 0.0;
4 double timeEnd = 25;
5 int numberOfPoints = 200;
6 
7 m = gillespieOnGridEx (rrHandle, timeStart, timeEnd, numberOfPoints);
Parameters
[in]handleHandle to a RoadRunner instance
[in]timeStartTime start
[in]timeEndTime end
[in]numberOfPointsFixed number of points to generate
Returns
Returns an array (RRCDataPtr) of columns containing the results of the simulation including string labels for the individual columns. The client is responsible for freeing the resulting RRCDataPtr structure.
bool setSeed ( RRHandle  handle,
long  seed 
)

Set the current seed used by the random generator.

Parameters
[in]handleHandle to a RoadRunner instance
[out]seedThis is the value the caller will set the seed to
Returns
Returns true if successful