applyChanges-methods: Generic Function to Apply Changes to Objects of Class...
In sybil: Efficient Constrained Based Modelling

Description Usage Arguments Value Methods Author(s) See Also

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.

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

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

`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`.

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).

signature(object = "sysBiolAlg"): Method used with objects extending class sysBiolAlg
signature(object = "sysBiolAlg_room"): Method used with objects of class sysBiolAlg_room

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

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

Class sysBiolAlg and resetChanges

sybil documentation built on May 31, 2021, 5:08 p.m.