Get the steady-state values of species and state variable parameters.

Usage

getSteadyState(
  quantitiesPaths = NULL,
  simulations,
  steadyStateTime,
  ignoreIfFormula = TRUE,
  stopIfNotFound = TRUE,
  lowerThreshold = 1e-15,
  simulationRunOptions = NULL
)

Arguments

quantitiesPaths: List of quantity paths (molecules and/or parameters) for which the steady-state will be simulated. If NULL (default), all molecules and state variable parameters are considered. The same list is applied for all simulations.
simulations: Simulation object or a list of Simulation objects
steadyStateTime: Simulation time (minutes). Must be long enough for system to reach a steady-state. 1000 by default. Either a single value (will be applied for all simulations), or a vector of values specific for each simulation. In latter case, must have equal size as simulations.
ignoreIfFormula: If TRUE (default), species and parameters with initial values defined by a formula are not included.
stopIfNotFound: Boolean. If TRUE (default), an error is thrown when results for certain species were not generated. This may happen when due to numerical problems some values cannot be calculated, though the whole simulation converges. Setting this argument to FALSE allows to ignore such errors. Check the outputs for empty values when using this option.
lowerThreshold: Numerical value (in default unit of the output). Any steady-state values below this value are considered as numerical noise and replaced by 0. If lowerThreshold is NULL, no cut-off is applied. Default value is 1e-15.
simulationRunOptions: Optional instance of a SimulationRunOptions used during the simulation run.

Value

A named list, where the names are the IDs of the simulations and the entries are lists containing paths and their values at the end of the simulation.

Details

The steady-state is considered to be the last value of the simulation with sufficiently long simulation time, i.e., where the rates of the processes do not (significantly) change.