sybil (version 2.2.0)

applyChanges-methods: Generic Function to Apply Changes to Objects of Class sysBiolAlg

Description

Use method applyChanges to apply changes in objects of class '>sysBiolAlg. Changes can be coefficients of the objective function, variable bounds or the optimization direction.

Usage

# S4 method for sysBiolAlg
applyChanges(object, del, obj, ld,
             react    = NULL,
             lb       = NULL,
             ub       = NULL,
             obj_coef = NULL,
             fldind   = TRUE,
             lpdir    = NULL)
# S4 method for sysBiolAlg_room
applyChanges(object, del, obj, ld,
             react    = NULL,
             lb       = NULL,
             ub       = NULL,
             obj_coef = NULL,
             fldind   = TRUE,
             lpdir    = NULL)

Arguments

object

An object of class '>sysBiolAlg.

del

A logical value indicating whether variable bounds should be altered or not.

obj

A logical value indicating whether objective coefficients should be altered or not.

ld

A logical value indicating whether the direction of optimization should be altered or not.

react

A numeric vector containing indices to reactions which should be changed (in terms of variable bounds or objective coefficients). Default: NULL.

lb

Numeric vector of the same length as react, containing the new lower variable bounds. Default: NULL.

ub

Numeric vector of the same length as react, containing the new upper variable bounds. Default: NULL.

obj_coef

Numeric vector of the same length as react, containing the new objective coefficients. Default: NULL.

fldind

Boolean value. If set to TRUE, (default) indices in "react" are used only for reactions. If set to FALSE, indices in "react" are used for all variables during optimization, e.g. also for additional variables introduced by the mtf algorithm. Currently unused by class '>sysBiolAlg_room. Default: TRUE.

lpdir

A single character value indicating the new direction of optimization. Default: NULL.

Value

Returns a list containing the original values in order to undo the changes with resetChanges:

fi

A numeric vector containing variable id's to apply changes to.

lb

A numeric vector of the same length as react containing the original variable lower bounds.

ub

A numeric vector of the same length as react containing the original variable upper bounds.

obj_coef

A numeric vector of the same length as react containing the original objective coefficients.

lpdir

A single character value giving the original optimization direction.

ri

A numeric vector of the same length as react containing row indices of the stoichiometric matrix required to apply changes in variable bounds when algorithm "room" is used. (only used by the '>sysBiolAlg_room method).

ci

A numeric vector of the same length as react containing column indices of the stoichiometric matrix required to apply changes in variable bounds when algorithm "room" is used. (only used by the '>sysBiolAlg_room method).

Methods

signature(object = "sysBiolAlg")

Method used with objects extending class '>sysBiolAlg

signature(object = "sysBiolAlg_room")

Method used with objects of class '>sysBiolAlg_room

See Also

Class '>sysBiolAlg and resetChanges