BacArena (version 1.0.1)

checkPhen: Function for checking phenotypes in the environment

Description

The generic function checkPhen checks and adds the phenotypes of organisms in the environment.

Usage

checkPhen(object, org, cutoff = 1e-06)
"checkPhen"(object, org, cutoff = 1e-06)

Arguments

object

An object of class Arena.

org

An object of class Organism.

cutoff

A number giving the cutoff for values of the objective function and fluxes of exchange reactions.

Value

Returns a number indicating the number of the phenotype in the phenotype list.

Details

The phenotypes are defined by flux through exchange reactions, which indicate potential differential substrate usages. Uptake of substances are indicated by a negative and production of substances by a positive number.

See Also

Arena-class and getPhenotype

Examples

data(Ec_core, envir = environment()) #get Escherichia coli core metabolic model
bac <- Bac(Ec_core,deathrate=0.05,
           growthlimit=0.05,growtype="exponential") #initialize a bacterium
arena <- Arena(n=20,m=20) #initialize the environment
checkPhen(arena,bac) #returns 1 as the index of the current phenotype in the list.