CNORode (version 1.14.0)

simulate: Simulate value signals a CNO list With Logic-Based ODEs.

Description

This function receives a set of inputs, namely the cnolist and the model and returns a list with the same size of the cnolist$valueSignals.

Usage

simulate(cnolist, model, ode_parameters=NULL, indices=NULL,
	adjMatrix=NULL, time=1, verbose=0, transfer_function=3,
	reltol=1e-04, atol=0.001, maxStepSize=Inf, maxNumSteps=1e+05, 
	maxErrTestsFails=50)

Arguments

cnolist

A list containing the experimental design and data.

model

A list with the ODEs parameter information. Obtained with createLBodeContPars.

ode_parameters

A list with the ODEs parameter information. Obtained with makeParameterList function.

indices

Indices to map data in the model. Obtained with indexFinder function from CellNOptR.

adjMatrix

The adjacency matrix. Recomputed if not provided

time

An integer with the index of the time point to start the simulation. Default is 1.

verbose

A logical value that triggers a set of comments.

transfer_function

The type of used transfer. Use 1 for no transfer function, 2 for Hill function and 3 for normalized Hill function.

reltol

Relative Tolerance for numerical integration.

atol

Absolute tolerance for numerical integration.

maxStepSize

The maximum step size allowed to ODE solver.

maxNumSteps

The maximum number of internal steps between two points being sampled before the solver fails.

maxErrTestsFails

Specifies the maximum number of error test failures permitted in attempting one step.

Value

Returns a list with simulated data that has the same structure as the cnolist$valueSignals. One matrix for each time-point.

Details

Check CellNOptR for details about the cnolist and the model format. For more details in the configuration of the ODE solver check the CVODES manual.

See Also

CellNOptR parEstimationLBode parEstimationLBodeSSm

Examples

library(CNORode)
data("ToyCNOlist",package="CNORode");
data("ToyModel",package="CNORode");
data("ToyIndices",package="CNORode");
dataSimulation = simulate(cnolistCNORodeExample, model,indices=indices);