sysBiolAlg: 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. 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).

Value

An instance of a subclass of class sysBiolAlg.

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 arguemts prefix and algorithm are stick together separated by sep (default: a single underscore "_"): prefix_algorithm. Additional arguments required by the initialize method are for example solver, method and solverParm.

Examples

Run this code

## 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")