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R

r - Variable in class org.simulator.sbml.astnode.ReactionValue
The corresponding reaction
randomInt(int, int) - Static method in class org.simulator.math.RNG
Generates a random integer between first and second input value.
RateRuleObject - Class in org.simulator.sbml.astnode
This class can compute and store the value of a rate rule together with the variable of the rule.
RateRuleObject(ASTNodeObject, int) - Constructor for class org.simulator.sbml.astnode.RateRuleObject
 
RateRuleObject(ASTNodeObject, int, Species, int, boolean, ValueHolder) - Constructor for class org.simulator.sbml.astnode.RateRuleObject
Constructor for a rule with a species as variable
RateRuleObject(ASTNodeObject, int, List<Integer>, ValueHolder) - Constructor for class org.simulator.sbml.astnode.RateRuleObject
Constructor for a rule with a compartment as variable
ReactionValue - Class in org.simulator.sbml.astnode
This class computes and stores values of ASTNodes that refer to a reaction.
ReactionValue(ASTNodeInterpreterWithTime, ASTNode, Reaction) - Constructor for class org.simulator.sbml.astnode.ReactionValue
 
real - Variable in class org.simulator.sbml.astnode.ASTNodeObject
The real value of the corresponding ASTNode
recovered(double) - Method in class org.simulator.sbml.EventInProcess
The trigger of the associated event has made a transition from true to false, so the event can be triggered again.
refresh() - Method in class org.simulator.sbml.astnode.StoichiometryObject
Refreshes the stoichiometry.
refresh(boolean) - Method in class org.simulator.sbml.EventInProcess
 
refresh(double) - Method in class org.simulator.sbml.EventInProcess
Refreshes the status of the event regarding the current time.
refresh(boolean) - Method in class org.simulator.sbml.EventInProcessWithDelay
 
refresh(double) - Method in class org.simulator.sbml.EventInProcessWithDelay
 
registerDelayValueHolder(DelayValueHolder) - Method in interface org.simulator.math.odes.DelayedDESystem
 
registerDelayValueHolder(DelayValueHolder) - Method in class org.simulator.sbml.SBMLinterpreter
 
RELMIN - Static variable in class org.simulator.math.odes.RosenbrockSolver
the minimum acceptable value of relTol - attempts to obtain higher accuracy than this are usually very expensive
relTol - Variable in class org.simulator.math.odes.AdaptiveStepsizeIntegrator
Default relative allowable vectorial tolerance.
removeBlock(int) - Method in class org.simulator.math.odes.MultiTable
Removes the MultiTable.Block with the given index from this data structure.
removePropertyChangeListener(PropertyChangeListener) - Method in class org.simulator.math.odes.AbstractDESSolver
 
removePropertyChangeListener(PropertyChangeListener) - Method in interface org.simulator.math.odes.DESSolver
remove PropertyChangedListener to this Solver
reset() - Method in class org.simulator.math.odes.AbstractDESSolver
Initialize with default integration step size and non-negative attribute true.
reset() - Method in class org.simulator.sbml.astnode.ASTNodeObject
Resets the node
resetState(double, double[]) - Method in class org.simulator.math.odes.AbstractDESSolver
 
RichDESystem - Interface in org.simulator.math.odes
A RichDESystem is a DESystem that provides additional information besides the pure rate of change during its evaluation.
rightChild - Variable in class org.simulator.sbml.astnode.ASTNodeObject
The ASTNodeObject of the right child of the corresponding ASTNode
RNG - Class in org.simulator.math
A Random Number Generator.
RNG() - Constructor for class org.simulator.math.RNG
 
root(ASTNodeObject, ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
root(double, ASTNodeObject, double) - Method in class org.simulator.sbml.astnode.ASTNodeInterpreterWithTime
 
root(ASTNode, ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
root(double, ASTNode) - Method in class org.simulator.sbml.ASTNodeInterpreter
 
root(ASTNode, ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
root(double, ASTNode) - Method in class org.simulator.sbml.EfficientASTNodeInterpreter
 
RootFunctionValue - Class in org.simulator.sbml.astnode
This class computes and stores values of ASTNodes that refer to a root function.
RootFunctionValue(ASTNodeInterpreterWithTime, ASTNode) - Constructor for class org.simulator.sbml.astnode.RootFunctionValue
 
RosenbrockSolver - Class in org.simulator.math.odes
RosenbrockSolver implements the Rosenbrock method to approximate ODE solutions.
RosenbrockSolver() - Constructor for class org.simulator.math.odes.RosenbrockSolver
default constructor
RosenbrockSolver(int, double) - Constructor for class org.simulator.math.odes.RosenbrockSolver
 
RosenbrockSolver(RosenbrockSolver) - Constructor for class org.simulator.math.odes.RosenbrockSolver
clone constructor
RuleObject - Class in org.simulator.sbml.astnode
This class can compute and store the value of a rule together with the variable of the rule.
RuleObject(ASTNodeObject, int) - Constructor for class org.simulator.sbml.astnode.RuleObject
 
RuleObject(ASTNodeObject, int, Species, int, boolean, ValueHolder) - Constructor for class org.simulator.sbml.astnode.RuleObject
Constructor for rules that refer to a species.
ruleObjects - Variable in class org.simulator.sbml.EventInProcess
 
RungeKutta_EventSolver - Class in org.simulator.math.odes
Runge-Kutta method.
RungeKutta_EventSolver() - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver
default constructor
RungeKutta_EventSolver(double) - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver
 
RungeKutta_EventSolver(double, boolean) - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver
 
RungeKutta_EventSolver(RungeKutta_EventSolver) - Constructor for class org.simulator.math.odes.RungeKutta_EventSolver
clone constructor

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