exhaustive {CellNOptR} | R Documentation

## Exhaustive search over the optimisation of a PKN model on MIDAS data.

### Description

This function performs an exhaustive search of the parameter space tring all the solutions. It is used internally by the genetic algorithm when a small model has to be optimised and the number of solutions to try is smaller than the number of iterations that the Genetic Algorithm will perform.

### Usage

    exhaustive(CNOlist, model, shuffle=FALSE, Nmax=NULL, verbose=TRUE, sizeFac =
    0.0001, NAFac = 1, relTol=0.1, timeIndex=2)

### Arguments

`CNOlist` | a CNOlist on which the score is based (based on valueSignals[[2]], i.e. data at time 1)
`model` | a model structure, as created by `readSIF`, normally pre-processed but that is not a requirement of this function
`shuffle` | The list of bitstrings is set up arbitrarely. You may want to shuffle it.
`Nmax` | The total number of computation will be 2 to the power N, where N is the size of the model (ReacID field). The total number of computation can be large. You may want to set a maximumn number of computation using Nmax.
`sizeFac` | the scaling factor for the size term in the objective function, default to 0.0001
`NAFac` | the scaling factor for the NA term in the objective function, default to 1
`relTol` | the relative tolerance for the best bitstring reported by the genetic algorithm, i.e., how different from the best solution, default set to 0.1 Not yet implemented.
`verbose` | logical (default to TRUE) do you want the statistics of each generation to be printed on the screen?
`timeIndex` | the index of the time point to optimize. Must be greater or equal to 2 (1 corresponds to time=0). Must be less than the number of time points. Default is 2.

### Value

This function returns a list with elements:

`bString` | the best bitstring
`bScore` | the best score
`all_scores` | all scores that have been computed
`results` | a matrix with columns "Generation","Best_score","Best_bitString","Stall_Generation","Avg_Score_Gen","Best_score_Gen","Best_bit_Gen","Iter_time"
`stringsTol` | the bitstrings whose scores are within the tolerance
`stringsTolScores` | the scores of the above-mentioned strings

Note that the field results, is not yet populated but maybe in the future.

### Author(s)

T. Cokelaer

### See Also

gaBinaryT1

### Examples

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

    #pre-process model

    model = preprocessing(CNOlistToy, ToyModel)

    #optimise

    results <-exhaustive(
    	CNOlist=CNOlistToy,
    	model=model,
        shuffle=TRUE,
        Nmax=1000,
    	verbose=FALSE)

[Package CellNOptR version 1.38.0 Index]