summaryOptsol: Summarize Objects of Class Optsol

In SysBioChalmers/sybil: Efficient Constrained Based Modelling

Summarize Objects of Class Optsol

Description

Generates a quick overview of results of simulations stored in objects of class optsol.

Usage

  summaryOptsol(opt, mod, perc = 1, tol = SYBIL_SETTINGS("TOLERANCE"))

Arguments

opt	An object of class optsol.
mod	An object of class modelorg.
perc	A single numeric value in between zero and one indicating how close a flux value has to reach a flux boundary in order to be called “limiting”, see Details below. Default: 1.
tol	A tolerance value, see Details below. Default: SYBIL_SETTINGS("TOLERANCE").

Details

The function summaryOptsol generates a summary of the simulations resulting in the object given in argument opt. Both model id's, of the optsol object and of the modelorg object must be identical. The resulting object of class summaryOptsol contains information about the number of zeros and non-zeros in the flux distribution, the substrates and products and about the limiting reactions.

A reaction i is called “limiting”, if its flux value v_i is non-zero: |v_i| > \mathit{tol} and if its flux value hits the flux boundaries: v_i \leq v_{i,\textrm{min}} \cdot \mathit{perc} \lor v_i \geq v_{i,\textrm{max}} \cdot \mathit{perc}.

Value

An object of class summaryOptsol if a flux distribution exists in argument opt, otherwise a summary of the objective values (mod_obj) is returned.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

Class optsol, class modelorg and class summaryOptsol.

SysBioChalmers/sybil documentation built on Aug. 24, 2023, 1:08 p.m.