Description Objects from the Class Slots Methods Author(s) See Also Examples

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.

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

`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.

`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.

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

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

`checkOptSol`

,
`optsol_optimizeProb`

`optsol_fluxdel`

,
`optsol_genedel`

,
`optsol_robAna`

and
`optsol_fluxVar`

1 | ```
showClass("optsol")
``` |

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