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

Usage

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

Arguments

simulations: Simulation object or a list or vector of Simulation objects to simulate. List or vector can be named (names must be uniques), in which case the names will reused in the output list. If not named, the output list will use simulation ids for names.
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.
steadyStateTime: Simulation time (minutes). In NULL (default), the default simulation time is the start time of the last application plus three days. The simulated time must be long enough for the system to reach a steady-state. Either a single value (will be applied for all simulations), or a list of values specific for each simulation. In latter case, must have equal size as simulations. When providing a list, NULL is allowed to calculate the time based on the last application.
ignoreIfFormula: If TRUE (default), species and parameters with initial values defined by a formula are not included.
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 values of the molecules amounts and state variable parameters in the simulation with sufficiently long simulation time, i.e., where the rates of the processes do not (significantly) change. The steady-state is NOT analytically calculated or estimated in any other way than simulating for the given time.

Examples

simPath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
sim <- loadSimulation(simPath)
steadyState <- getSteadyState(simulations = sim)
# Set initial values for steady-state simulations
setQuantityValuesByPath(
  quantityPaths = steadyState[[sim$id]]$paths,
  values = steadyState[[sim$id]]$values, simulation = sim
)