prep4simFuzzy: Prepare a model for simulation

In saezlab/CNORfuzzy: Addon to CellNOptR: Fuzzy Logic

Description

Adds to the model some fields that are used by the simulation engine and calls prep4sim function from CellNOptR package

Usage

prep4simFuzzy(model, paramsList, verbose=TRUE)

Arguments

model	A model, as output by readSIF, normally pre-processed but that is not a requirement of this function.
paramsList	A parameters list that must contain at least the CNOlist parameter in the Data field (param = list(data=cnolist)) and possibly optional arguments related to the fuzzy logic (see defaultParametersFuzzy)
verbose	a verbose option set to TRUE by default.

Details

This adds fields that are necessary for the simulation engine for both Boolean and constrained Fuzzy logic simulation.

Value

In addition to the fields returned by the prep4sim function of CellNOptR, this function appends the following fields:

finalCube	stores, for each reac(row) the location of its inputs (col)
ixNeg	stores, for each reac(row) and each input (col) whether it is a negative input
ignoreCube	logical matrix of the same size as the 2 above, that tells whether the particular cell is filled or not
maxIx	row vector that stores, for each reac, the location of its output
modelname	stores the name of the model from which these fields were derived

Author(s)

C. Terfve, modified by M.K. Morris and T. Cokelaer

See Also

simFuzzyT1

Examples

    data(ToyModel, package="CellNOptR")
    data(CNOlistToy, package="CellNOptR")
    params <- defaultParametersFuzzy()
    params$data = CNOlistToy
    fields4sim <- prep4simFuzzy(ToyModel, params)

saezlab/CNORfuzzy documentation built on May 3, 2019, 1:49 p.m.