solveStoch: Model simulation (stochastic simulation)

In Vessy/sysBio: A package for modeling biological systems

Description

This function allows users to simulate the model (i.e., solve ODEs) using Gillespie stochastic simulation algorithm (using the "ssa" function from the GillespieSSA package).

Usage

solveStoch(x, times = 10, method = "D", simName = "", tau = 0.3,
  f = 10, epsilon = 0.03, nc = 10, hor = NaN, dtf = 10, nd = 100,
  ignoreNegativeState = TRUE, consoleInterval = 0, censusInterval = 0,
  verbose = FALSE, maxWallTime = Inf)

Arguments

x	model name (required)
times	time points in which model will be simulated
method	text string indicating the SSA method to use (see ?GillespieSSA::ssa for more details)
simName	see ?GillespieSSA::ssa for more details
tau	see ?GillespieSSA::ssa for more details
f	see ?GillespieSSA::ssa for more details
epsilon	see ?GillespieSSA::ssa for more details
nc	see ?GillespieSSA::ssa for more details
hor	see ?GillespieSSA::ssa for more details
dtf	see ?GillespieSSA::ssa for more details
nd	see ?GillespieSSA::ssa for more details
ignoreNegativeState	see ?GillespieSSA::ssa for more details
consoleInterval	see ?GillespieSSA::ssa for more details
censusInterval	see ?GillespieSSA::ssa for more details
verbose	see ?GillespieSSA::ssa for more details
maxWallTime	see ?GillespieSSA::ssa for more details

Value

Data frame where each row corresponds to a time point in which model was simulated. First column corresponds to time, while the rest of columns correspond to model species, i.e., values assigned to those species at a given time point.

Examples

exmp <- newModel("This is an example of a new model")
addMAreaction(exmp, react="A = null", "rf", "rb")
addMAreaction(exmp, react="A + B -> 2*AB", "k", name="Forward AB")
addMAreaction(exmp, react="AB -> null", "rAB")

addMAreactRate(exmp, "rf", "fixed", "1")
addMAreactRate(exmp, "rb", "fixed", "0.75")
addMAreactRate(exmp, "k", "fixed", "0.5")
addMAreactRate(exmp, "rAB", "assigned", "p1*A")

addParameters(exmp, "p1", 0.75)
 
addSpecies(exmp, "A", 10)
addSpecies(exmp, "B", 10)
addSpecies(exmp, "AB", 0)

addRule(exmp, "rule B", "ODEs", "B=-0.1*AB")

makeModel(exmp)
  
simResults.stoch <- solveStoch(exmp)
plotResults(simResults.stoch, title="Simulation results (stochastic)")

Vessy/sysBio documentation built on May 9, 2019, 9:55 p.m.