Package fern.simulation.algorithm

Provides algorithms for stochastic simultion of reaction networks.

See:
          Description

Class Summary
AbstractBaseTauLeaping Base class for all tau leaping procedures (which are different in the methods choosing the timestep candidates for critical and noncritical reactions).
AbstractTauLeapingPropensityBoundSimulator There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.
CompositionRejection This is an enhanced version of the original Direct method developed by Gillespie.
DependencyGraph Implements a dependency graph.
GibsonBruckSimulator Implementation of the algorithm of Gibson and Bruck.
GillespieEnhanced This is an enhanced version of the original Direct method developed by Gillespie.
GillespieSimple Implementation of Gillespie's Direct method.
GroupContainer  
HybridMaximalTimeStep This is an modified version of Maximal Time Step Method by Puchalka and Kierzec.
IndexedPriorityQueue Implements an indexed priority queue.
TauLeapingAbsoluteBoundSimulator There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.
TauLeapingRelativeBoundSimulator There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.
TauLeapingSpeciesPopulationBoundSimulator There are some possibilities to bind the expected change of the propensities by a value epsilon in order to fulfill the leap condition.
 

Package fern.simulation.algorithm Description

Provides algorithms for stochastic simultion of reaction networks.