getLBodeModelSim: Simulate the logic-based ODE model

Description

This function simulates a logic-based ODE model and return a list with one matrix for each time point. The input species in the model are filled with NA values. If the simulation of a particular set of initial conditions fails the solver will fill the experience row with NA values.

Usage

getLBodeModelSim(cnolist, model, ode_parameters = NULL, indices = NULL, timeSignals=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

The logic model to be simulated.

ode_parameters

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

indices

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

timeSignals

An array containing a different timeSignals. If you use this argument, it will also modify the dimensions from valueSignals.

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

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 with similar structure to cnolist$valueSignals. Contains one matrix for each time-point. Each matrix contains one row per experiment and one columns per model species.

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.

Examples

Run this code

library(CNORode)
data('ToyCNOlist',package='CNORode');
data('ToyModel',package='CNORode');
data('ToyIndices',package='CNORode');
modelSimulation=getLBodeModelSim(cnolistCNORodeExample, model,indices=indices);