defaultParametersFuzzy: Create a list of default parameters

In saezlab/CNORfuzzy: Addon to CellNOptR: Fuzzy Logic

Description

Parameters are required at different levels in the Fuzzy optimisation. This function provides a list with all parameters that are necessary.

Usage

defaultParametersFuzzy(data=NA, model=NA, nTF=7)

Arguments

data	the CNOlist that contains the data that you will use
model	the model that you want to optimise
nTF	number of discrete values to be used for each transfer function parameter.

Details

The list contains 3 types of parameters:

• Fuzzy parameters (e.g, Type1Funs, Type2Funs, RedThresh, DoRefinement)

• GA parameters similar to those used in CellNOptR package (see gaDiscreteT1 or defaultParametersFuzzy

• optimisation parameters related to the refinement step.

  1. algorithm='NLOPT_LN_SBPLX'

  2. xtol_abs=0.001

  3. maxEval=1000

  4. maxTime=5*60

• In addition, you can set Model and Data (CNOlist).

Value

params

a list of default parameters.

Author(s)

T. Cokelaer

Examples

    data(ToyModel,package="CellNOptR")
    data(CNOlistToy,package="CellNOptR")
    params = defaultParametersFuzzy(CNOlistToy, ToyModel)

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