sysBiolAlg {sybil}R Documentation

General Constructor Function For Objects of Class sysBiolAlg

Description

This function serves as a user constructor function for objects of class sysBiolAlg.

Usage

  sysBiolAlg(model,
             algorithm = SYBIL_SETTINGS("ALGORITHM"),
             prefix = "sysBiolAlg", sep = "_",
             ...)

Arguments

model

An object of class modelorg.

algorithm

A single character string giving the name of the algorithm to use. See parameter "ALGORITHM" in SYBIL_SETTINGS for possible values.
Default: SYBIL_SETTINGS("ALGORITHM").

prefix

A single character string containing a prefix for the new class name.
Default: "sysBiolAlg".

sep

A single character string containing a separator for prefix and algorithm.
Default: "_".

...

Further arguments passed to the initialize method depending on the desired algorithm (see Details below).

Details

If argument algorithm is set to "foo" and prefix is set to "sysBiolAlg" (default), sysBiolAlg will try to build an instance of class sysBiolAlg_foo. If no such class definition exists, an error will be returned. For the name of the class, the values of arguments prefix and algorithm are stick together separated by the value of argument sep: prefix_algorithm.

Additional arguments required by the initialize method are for example solver, method and solverParm.

Value

An instance of a subclass of class sysBiolAlg.

Author(s)

Gabriel Gelius-Dietrich <geliudie@uni-duesseldorf.de>

Maintainer: Mayo Roettger <mayo.roettger@hhu.de>

See Also

Class sysBiolAlg

Examples

## Not run: 
## The examples here require the package glpkAPI to be
## installed. If that package is not available, you have to set
## the argument 'solver' (the default is: solver = SYBIL_SETTINGS("SOLVER")).

data(Ec_core)

## algorithm: fba (flux balance analysis)
fb <- sysBiolAlg(Ec_core, algorithm = "fba")

## algorithm: lmoma (linearized version of MOMA)
fb <- sysBiolAlg(Ec_core, algorithm = "lmoma")

## End(Not run)

[Package sybil version 2.2.0 Index]