changeFobj: Function for changing the objective function of the model

In euba/BacArena: Modeling Framework for Cellular Communities in their Environments

Function for changing the objective function of the model

Description

The generic function changeFobj changes the objective function, which is used for the linear programming in optimizeLP.

Usage

changeFobj(object, new_fobj, model, alg = "fba")

## S4 method for signature 'Human'
changeFobj(object, new_fobj, model, alg = "fba")

Arguments

object	An object of class Human.
new_fobj	A character vector giving the reaction name of the new objective function.
model	The original model structure which is converted into a problem object used for the next optimization.
alg	A character vector giving the algorithm which should be used for the optimization (default is flux balance analysis).

Details

To avoid the bias to just one particular objective function, the objective can be changed dynamically in this function.

See Also

Human-class and optimizeLP

Examples

data(Ec_core, envir = environment()) #get Escherichia coli core metabolic model
human <- Human(Ec_core,deathrate=0.05,
           minweight=0.05,growtype="exponential") #initialize a bacterium
changeFobj(human,'EX_glc(e)',Ec_core)

euba/BacArena documentation built on March 27, 2024, 2:33 p.m.