simulate {CNORode} | R Documentation |
This function receives a set of inputs, namely the cnolist and the model and returns a list with the same size of the cnolist$valueSignals.
simulate(cnolist, model, ode_parameters=NULL, indices=NULL, adjMatrix=NULL, time=1, verbose=0, transfer_function=3, reltol=1e-04, atol=0.001, maxStepSize=Inf, maxNumSteps=1e+05, maxErrTestsFails=50)
cnolist |
A list containing the experimental design and data. |
model |
A list with the ODEs parameter information. Obtained with |
ode_parameters |
A list with the ODEs parameter information. Obtained with makeParameterList function. |
indices |
Indices to map data in the model. Obtained with indexFinder function from CellNOptR. |
adjMatrix |
The adjacency matrix. Recomputed if not provided |
time |
An integer with the index of the time point to start the simulation. Default is 1. |
verbose |
A logical value that triggers a set of comments. |
transfer_function |
The type of used transfer. Use 1 for no transfer function, 2 for Hill function and 3 for normalized Hill function. |
reltol |
Relative Tolerance for numerical integration. |
atol |
Absolute tolerance for numerical integration. |
maxStepSize |
The maximum step size allowed to ODE solver. |
maxNumSteps |
The maximum number of internal steps between two points being sampled before the solver fails. |
maxErrTestsFails |
Specifies the maximum number of error test failures permitted in attempting one step. |
Check CellNOptR
for details about the cnolist and the model format.
For more details in the configuration of the ODE solver check the CVODES manual.
Returns a list with simulated data that has the same structure as the cnolist$valueSignals. One matrix for each time-point.
David Henriques, Thomas Cokelaer
CellNOptR
parEstimationLBode
parEstimationLBodeSSm
library(CNORode) data("ToyCNOlist",package="CNORode"); data("ToyModel",package="CNORode"); data("ToyIndices",package="CNORode"); dataSimulation = simulate(cnolistCNORodeExample, model,indices=indices);