CNORwrapFuzzy: CNORfuzzy analysis wrapper

In saezlab/CNORfuzzy: Addon to CellNOptR: Fuzzy Logic

Description

This function is a wrapper around the whole CNOR Fuzzy analysis. It performs the following steps:

1. Plot the CNOlist

2. Checks data to model compatibility

3. Pre-processing steps

4. Prepare for simulation (see prep4simFuzzy)

5. Optimisation using Fuzzy transfer function (see gaDiscreteT1)

6. Refinement and reduction steps (see getRefinedModel and reduceFuzzy).

Usage

CNORwrapFuzzy(data, model, paramsList=NULL, verbose=TRUE)

Arguments

data	a CNOlist structure (as created by makeCNOlist) that contains the data that you will use (see readMIDAS and readSIF from CellNOptR).
model	the model that you want to optimise
paramsList	Use defaultParametersFuzzy function to create a template. Entries are 3-types: (i) GA algorithm parameters for the optimisation, (ii) Fuzzy parameters for the transfer functions and (iii) internal optimisation parameters within the refinement step. See defaultParametersFuzzy function for details on the parameters.
verbose

Details

If you do not provide a parameter list argument, defaultParametersFuzzy is called internally to populate the paramsList argument.

Value

This function returns an object containing the results that can be used by other functions such as compileRes.

Author(s)

M.K. Morris

References

CNORWrap function from CellNOptR package

See Also

defaultParametersFuzzy, compileMultiRes

Examples

    # Load some data
    data(CNOlistToy, package="CellNOptR")
    data(ToyModel, package="CellNOptR")
    # Get some default parameters to play with, limiting the duration of the GA
    # algorithm and optimisation step
    paramsList = defaultParametersFuzzy() 
    paramsList$maxTime = 20
    paramsList$optimisation$maxtime = 10
    results = CNORwrapFuzzy(CNOlistToy, ToyModel, paramsList)

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