optsol-class: Class optsol

In sybil: Efficient Constrained Based Modelling

Description

The class optsol provides data structures to store and access the results of optimizations. This class is extended by other classes and will not be used as is. The representation of class optsol is used as superclass.

Objects from the Class

A virtual Class: No objects may be created from it.

Slots

mod_id:

Object of class "character" containing the model id of the used model.

mod_key:

Object of class "character" containing the model key of the used model.

solver:

Object of class "character" indicating the used solver.

method:

Object of class "character" indicating the used method.

algorithm:

Object of class "character" containing the name of the algorithm used for optimizations.

num_of_prob:

Object of class "integer" indicating the number of optimization problems.

lp_num_cols:

Object of class "integer" indicating the number of columns.

lp_num_rows:

Object of class "integer" indicating the number of rows.

lp_obj:

Object of class "numeric" containing the optimal values of the objective function after optimization. If no flux distribution is available, slot lp_obj contains the cross-product of the objective coefficients in slot obj_coef and the part of the flux distribution in slot fluxdist containing the values representing fluxes in the entire metabolic network (slot fldind).

lp_ok:

Object of class "integer" containing the exit code of the optimization.

lp_stat:

Object of class "integer" containing the solution status of the optimization.

lp_dir:

Object of class "character" indicating the direction of optimization.

obj_coef:

Object of class "numeric" containing the objective coefficients of the used model (slot obj_coef of an object of class modelorg). These are not necessarily the objective coefficients of the used algorithm.

obj_func:

Object of class "character" containing the objective function of the used model. Usually, it contains the return value of printObjFunc.

fldind:

Object of class "integer" pointers to columns (variables) representing a flux (reaction) in the original network. The variable fldind[i] in the problem object represents reaction i in the original network.

fluxdist:

Object of class "fluxDistribution" containing the solutions flux distributions.

alg_par:

Object of class "list" containing a named list containing algorithm specific parameters.

Methods

algorithm<-:

signature(object = "optsol"): sets the algorithm slot.

algorithm:

signature(object = "optsol"): gets the algorithm slot.

alg_par

signature(object = "optsol"): gets the alg_par slot.

alg_par<-

signature(object = "optsol"): sets the alg_par slot.

checkStat:

signature(opt = "optsol"): returns the indices of problems with a non optimal solution status.

fldind<-:

signature(object = "optsol"): sets the fldind slot.

fldind:

signature(object = "optsol"): gets the fldind slot.

fluxdist<-:

signature(object = "optsol"): sets the fluxdist slot.

fluxdist:

signature(object = "optsol"): gets the fluxdist slot.

fluxes<-:

signature(object = "optsol"): sets the fluxes slot of slot fluxdist.

fluxes:

signature(object = "optsol"): gets the fluxes slot of slot fluxdist.

plot:

signature(x = "optsol"): plots a histogram of the values of the objective function given in the model in optimal state. Additional arguments can be passed to histogram via the ... argument.

length:

signature(x = "optsol"): returns the number of optimizations.

lp_dir<-:

signature(object = "optsol", value = "character"): sets the lp_dir slot. Argument value can be "min" (minimization) or "max" (maximization).

lp_dir<-:

signature(object = "optsol", value = "factor"): sets the lp_dir slot.

lp_dir<-:

signature(object = "optsol", value = "numeric"): sets the lp_dir slot. Argument value can be 1 (minimization) or -1 (maximization).

lp_dir:

signature(object = "optsol"): gets the lp_dir slot.

lp_num_cols<-:

signature(object = "optsol"): sets the lp_num_cols slot.

lp_num_cols:

signature(object = "optsol"): gets the lp_num_cols slot.

lp_num_rows<-:

signature(object = "optsol"): sets the lp_num_rows slot.

lp_num_rows:

signature(object = "optsol"): gets the lp_num_rows slot.

lp_obj<-:

signature(object = "optsol"): sets the lp_obj slot.

lp_obj:

signature(object = "optsol"): gets the lp_obj slot.

lp_ok<-:

signature(object = "optsol"): sets the lp_ok slot.

lp_ok:

signature(object = "optsol"): gets the lp_ok slot.

lp_stat<-:

signature(object = "optsol"): sets the lp_stat slot.

lp_stat:

signature(object = "optsol"): gets the lp_stat slot.

method<-:

signature(object = "optsol"): sets the method slot.

method:

signature(object = "optsol"): gets the method slot.

mod_id<-:

signature(object = "optsol"): sets the mod_id slot.

mod_id:

signature(object = "optsol"): gets the mod_id slot.

mod_key<-:

signature(object = "optsol"): sets the mod_key slot.

mod_key:

signature(object = "optsol"): gets the mod_key slot.

mod_obj:

signature(object = "optsol_fluxdel"): returns always the cross-product of the objective coefficients in slot obj_coef and the part of the flux distribution in slot fluxdist containing the values representing fluxes in the entire metabolic network (slot fldind). If slot obj_coef is NA, the content of slot lp_obj is returned. In contrast, method lp_obj always returns the value of the objective function of the used algorithm after optimization.

nfluxes:

signature(object = "optsol"): gets the number of elements in the flux distribution matrix.

num_of_prob<-:

signature(object = "optsol"): sets the num_of_prob slot.

num_of_prob:

signature(object = "optsol"): gets the num_of_prob slot.

obj_coef<-:

signature(object = "optsol"): sets the obj_coef slot.

obj_coef:

signature(object = "optsol"): gets the obj_coef slot.

obj_func<-:

signature(object = "optsol"): sets the obj_func slot.

obj_func:

signature(object = "optsol"): gets the obj_func slot.

react_id<-:

signature(object = "optsol"): sets the react_id slot.

react_id:

signature(object = "optsol"): gets the react_id slot.

show:

signature(object = "optsol"): prints a summary of the content of instance of class optsol.

solver<-:

signature(object = "optsol"): sets the solver slot.

solver:

signature(object = "optsol"): gets the solver slot.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

checkOptSol, optsol_optimizeProb optsol_fluxdel, optsol_genedel, optsol_robAna and optsol_fluxVar

Examples

  showClass("optsol")

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