getLBodeDataSim {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$valueSignals.
getLBodeDataSim(cnolist, model, ode_parameters = NULL, indices = NULL, timeSignals=NULL, time = 1, verbose = 0, transfer_function = 3, reltol = 1e-04, atol = 0.001, maxStepSize = Inf, maxNumSteps = 1e+05, maxErrTestsFails = 50, initial_state=0.1)
cnolist |
A list containing the experimental design and data. |
model |
A list with the ODEs parameter information. Obtained with |
ode_parameters |
A list with the ODEs parameter information. Obtained with makeParameterList function. |
indices |
Indices to map data in the model. Obtained with indexFinder function from CellNOptR. |
timeSignals |
An array containing a different timeSignals. If you use this argument, it will also modify the dimensions from valueSignals. |
time |
An integer with the index of the time point to start the simulation. Default is 1. |
verbose |
A logical value that triggers a set of comments. |
transfer_function |
The type of used transfer. Use 1 for no transfer function, 2 for Hill function and 3 for normalized Hill function. |
reltol |
Relative Tolerance for numerical integration. |
atol |
Absolute tolerance for numerical integration. |
maxStepSize |
The maximum step size allowed to ODE solver. |
maxNumSteps |
The maximum number of internal steps between two points being sampled before the solver fails. |
maxErrTestsFails |
Specifies the maximum number of error test failures permitted in attempting one step. |
initial_state |
initial state of the dynamic nodes (non-measured) (Defaults to 0.1) |
Check CellNOptR
for details about the cnolist and the model format.
For more details in the configuration of the ODE solver check the CVODES manual.
Returns a list with simulated data that has the same structure as the cnolist$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=getLBodeDataSim(cnolistCNORodeExample, model,indices=indices);